Immunoaffinity isolation of modified peptides from complex mixtures

ABSTRACT

The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS-MS), and/or MS 3  analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide. Also provided are an immunoaffinity isolation device comprising a modification-specific antibody, and antibodies against novel UFD1 and PTN6 phosphorylation sites.

RELATED APPLICATIONS

This application claims priority to U.S. Ser. No. 60/299,893, filed Jun.21, 2001, and U.S. Ser. No. 60/337,012, filed Nov. 8, 2001, bothabandoned, and is a continuation-in-part of U.S. Ser. No. 10/175,486,filed Jun. 19, 2002, presently pending, and U.S. Ser. No. 09/535,364,filed Mar. 24, 2000, presently pending, itself a continuation-in-part ofU.S. Ser. No. 09/148,712, filed Sep. 4, 1998, now issued, thedisclosures of which are hereby incorporated by reference herein.

FIELD OF THE INVENTION

The invention relates to peptides and methods of isolating andcharacterizing the same.

BACKGROUND OF THE INVENTION

The activation of proteins by modification represents an importantcellular mechanism for regulating most aspects of biologicalorganization and control, including growth, development, homeostasis,and cellular communication. For example, protein phosphorylation plays acritical role in the etiology of many pathological conditions anddiseases, including cancer, developmental disorders, autoimmunediseases, and diabetes. In spite of the importance of proteinmodification, it is not yet well understood at the molecular level. Thereasons for this lack of understanding are, first, that the cellularmodification system is extraordinarily complex, and second, that thetechnology necessary to unravel its complexity has not yet been fullydeveloped.

The complexity of protein modification on a proteome-wide scale derivesfrom three factors: the large number of modifying proteins, e.g.kinases, encoded in the genome, the much larger number of sites onsubstrate proteins that are modified by these enzymes, and the dynamicnature of protein expression during growth, development, disease states,and aging. The human genome encodes, for example, over 520 differentprotein kinases, making them the most abundant class of enzymes known.See Hunter, Nature 411: 355-65 (2001). Each of these kinasesphosphorylates specific serine, threonine, or tyrosine residues locatedwithin distinct amino acid sequences, or motifs, contained withindifferent protein substrates. Most kinases phosphorylate many differentproteins: it is estimated that one-third of all proteins encoded by thehuman genome are phosphorylated, and many are phosphorylated at multiplesites by different kinases. See Graves et al., Pharmacol. Ther.82:111-21 (1999).

Many of these phosphorylation sites regulate critical biologicalprocesses and may prove to be important diagnostic or therapeutictargets for molecular medicine. For example, of the more than 100dominant oncogenes identified to date, 46 are protein kinases. SeeHunter, supra. Oncogenic kinases such as ErbB2 and Jak3, widelyexpressed in breast tumors and various leukemias, respectively,transform cells to the oncogenic phenotype at least in part because oftheir ability to phosphorylate cellular proteins. Understanding whichproteins are modified by these kinases will greatly expand ourunderstanding of the molecular mechanisms underlying, e.g., oncogenictransformation. Thus, the ability to selectively identify modificationsites, e.g. phosphorylation sites, on a wide variety of cellularproteins represents an important new tool for understanding the keysignaling proteins and pathways implicated in diseases, such as cancer.

Although several methods for purifying phosphopeptides have beendescribed, these methods have significant limitations that render themunsuitable for the isolation or purification of modified peptides fromcomplex mixtures of peptides on a genome- or cell-wide basis. In onemethod, which employs reversed-phase HPLC, proteins are labeled in vivoor in vitro with radioactive phosphate, and the protein of interest ispurified to near homogeneity (so that it represents at least 95% of theprotein in the sample) before analysis. See, e.g. Wettenhall et al.Methods Enzymol. 201: 186-199 (1991). The highly purified protein isthen digested with a proteolytic enzyme to produce peptides, and theradioactively labeled peptides containing a phosphorylation site of thesingle protein are purified by reversed-phase HPLC. Phosphorylatedpeptides are distinguished from nonphosphorylated peptides by measuringthe radioactivity associated with each HPLC fraction, and thenchemically sequenced.

The reversed-phase HPLC method has several important limitations thatrender it unsuitable for the purification of modified peptides fromcomplex mixtures of peptides, e.g. cellular digests. The method cannotbe applied to biological samples that cannot be radioactively labeled,such as tissue biopsy samples. Selective peptide loss duringpurification by this method can introduce biases, so that the mostprominent modified peptide before and after the HPLC step is notnecessarily the same. This problem is addressed by first purifying theprotein so its level of radioactivity can be measured and thenrigorously accounting for sample recovery during all subsequentpurification and analysis steps. Accordingly, modified sites cannot beidentified from complex peptide mixtures. The HPLC method is oftenunsuccessful when applied to proteins that are modified at low levels,for example, where only a small percentage (less than 10%) of theprotein is phosphorylated at one site. This problem results from thedifficulty of purifying a phosphopeptide to homogeneity against a highbackground of nonphosphorylated peptides, and the need for a nearlyhomogenous phosphopeptide during chemical sequencing. Additionalshortcomings of this method exist.

Several researchers have employed immobilized phospho-specificantibodies, along with mass spectrometry (MS or MS/MS), to identifyphosphorylation sites in proteins. Immobilized anti-phosphotyrosineantibodies have been used to purify phosphopeptides from digests ofgelsolin, an actin binding-protein. See De Corte, et al., Prot. Sci. 8:234-241 (1999). However the single protein of interest, gelsolin, wasfirst purified and phosphorylated in vitro, before digesting to yieldgelsolin-specific phosphopeptides. Immobilized anti-phosphotyrosineantibodies have similarly been employed to identify EphB phosphopeptidesfrom purified EphB digests (Kalo et al., Biochem. 38:14396-408 (1999))and to purify alpha-enolase phosphopeptides from a purified digest ofhuman alpha-enolase (Marcus et al., Electrophoresis 21: 2622-2636(2000)). However, in the latter attempt the method failed, and theauthors expressly concluded that the low binding affinity between theantibody and the phosphopeptides makes the detection of phosphorylationsites almost impossible (Id. at p. 2635). The prevailing view(enunciated by Marcus et al.) that phosphospecific antibodies are notgenerally suitable for isolating phosphopeptides has recently beenreiterated in a review on protein phosphorylation analysis authored byrecognized leaders in the field of biological mass spectrometry. Mann etal., Trends in Biotech. 20: 261-268 (2002).

The identification of Ty1 Gag protein epitopes in digested yeast cellextract using an immobilized epitope-specific antibody has also beenreported. See Yu et al., J. Am. Soc. Mass. Spec. 9: 208-215 (1998).However, the immobilized antibody was a Tyl Gag epitope-specificantibody (i.e. was not a general modification-specific antibody), wasnot phospho-specific, and recognized only peptides from a singleprotein, Ty1 Gag. None of these methodologies are suitable for theselective isolation of phosphopeptides from complex mixtures of peptidesthat are derived from multiple, unpurified proteins, and most requirethe timely pre-purification of desired proteins. Reviewed in Mann etal., Ann. Rev. Biochem. 70:437-73 (2001).

Another widely used method for purifying modified peptides isimmobilized metal affinity chromatography (IMAC). This pseudo-affinitypurification method is based on the interaction of metal ions andnegatively charged peptide moieties, such as phosphate. See, e.g.Posewitz et al., Anal. Chem. 15: 2883-2892 (1999). Pre-purified,phosphorylated proteins are digested to peptides, and the phosphorylatedpeptides are then purified by passing the digest through a miniaturizedchromatography column containing a resin with a covalently attachedmetal chelator, e.g. iminodiacetic or nitrilotriacetic acid. A cation isnon-covalently attached to the chelator by treating the resin with oneof several metal salts, such as Fe³⁺, Ni²⁺, Ga³⁺, or Cu²⁺. When theprotein digest is applied to the column, peptides with a sufficientlyhigh negative charge density, such as from a phosphate group, can bindto the metal cation. Eluted peptides can then be analyzed by chemicalsequencing or by mass spectrometry (MS or MS/MS) to assignphosphorylation sites.

As with the reversed-phase HPLC method, IMAC purification of modifiedpeptides has several limitations that render it unsuitable for thepurification of modified peptides from complex mixtures of peptides,such as cellular digests. The method must be adjusted for each desiredsample, since, phosphopeptides, for example, are sensitive to the exactconditions used for IMAC. It is not unusual to test peptide binding toall 4 commonly used cations in combination with 3 different pHconditions (12 test conditions altogether) in order to find the metal-pHcombination best suited for purification of a single, specificphosphopeptide. Isolating a second, different phosphopeptide from thesame, or different, protein may require a second metal-pH combinationthat is unique. The IMAC method is not specific for phosphopeptides, andpeptides with several negatively charged amino acid residues (such asaspartic acid and glutamic acid) and without phosphate can bind to IMACresins and contaminate any purified phosphopeptides. This drawback isespecially problematic when only a small percentage of the proteinsample is modified, e.g. a partially phosphorylated protein, because thebackground level of contaminating nonphosphorylated peptides canoverwhelm the level of phosphopeptides. For this reason, the IMAC methodis not suitable for the isolation of desired modified peptides fromcomplex peptide mixtures. Further, the method is not specific for thetype of modified residue, e.g. phosphorylated residue, thus peptideswith phosphoserine, phosphothreonine, or phosphotyrosine all bind andelute from IMAC resins.

Accordingly, there remains a need in the art for the development ofsimple peptide isolation/purification methods that are suitable for theisolation of modified peptides from complex mixtures of peptides, e.g.digested cell extracts, which contain a wide variety of different,modified proteins, and yet do not require timely or costlypre-purification steps. The development of suitable peptide isolationmethods that are simple and can be readily automated would, for example,enable the rapid profiling of activation states on a genome-wide basisand the identification of new diagnostic or therapeutic targets withincell signaling pathways that are at the forefront of the proteomics eracurrently underway. The unresolved need for such high-throughput methodshas recently been recognized. See, e.g. Mann, Nat. Biotech. 17: 954-55(1999).

SUMMARY OF THE INVENTION

The present invention provides methods for isolating a modified peptidefrom a complex mixture of peptides (such as exists in a cell extractdigest) by the steps of: (a) obtaining a proteinaceous preparation froman organism, in which modified peptides from two or more differentproteins are present; (b) contacting the proteinaceous preparation withat least one immobilized modification-specific antibody; and (c)isolating at least one modified peptide specifically bound by theimmobilized modification-specific antibody. The method may furtherinclude the step of (d) characterizing the modified peptide(s) isolatedin step (c) by mass spectrometry (MS), tandem mass spectrometry (MS-MS),and/or MS³ analysis. The method may also further include the step of (e)utilizing a search program (such as Sequest) to substantially match thespectra obtained for the modified peptide(s) during the characterizationof step (d) with the spectra for a known peptide sequence, therebyidentifying the parent protein(s) of the modified peptide(s). Theinvention encompasses the isolation of modified peptides containingvirtually any type of modified amino acids, including but not limited tophosphorylated, acetylated, methylated, nitrosylated, and/orglycosylated residues. Motif-specific, context-independent antibodiesthat bind single modified amino acids or that bind conserved modifiedmotifs comprising multiple amino acids are advantageously employed inthe disclosed methods.

Also provided are an immunoaffinity isolation device for the isolationof modified peptides from a complex mixture according to the method ofthe invention, and antibodies to novel UFD1 and PTN6 phosphorylationsites discovered by the practice of the disclosed methods.

The method of the invention enables the rapid, efficient, and directisolation (and subsequent characterization) of modified peptides fromcomplex mixtures, such as crude cell extracts, without the need forcostly and timely pre-purification of desired peptides or proteins. Themethod enables the single-step immunoaffinity isolation, and subsequentcharacterization of multiple different modified peptides, correspondingto a multitude of different modified proteins and signaling pathways,with a single antibody. Alternatively, the method can further employ asimple pre-fractionation step. The simplicity of the disclosed methodalso renders it readily automatable, as only a single isolation step isrequired. Further advantages and preferred embodiments of the inventionare described in detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1—is a flow-diagram representation of the method of the invention.

FIG. 2—depicts a MALDI-TOF mass spectrum of an unpurified mixture of 10different phosphorylated and nonphosphorylated peptides, usingalpha-cyano-4-hydroxycinnamic acid as matrix. Peaks labeled with starsare phosphorylated peptides, and peaks labeled with circles correspondto nonphosphorylated peptides. Unmarked peaks are synthetic peptidebyproducts.

FIG. 3—depicts a MALDI-TOF mass spectrum of the phosphotyrosine peptidemixture described in FIG. 2, after isolation of phosphopeptides withmonoclonal P-Tyr-100 antibody-resin, according to the method of theinvention. Peaks labeled with stars are phosphorylated peptides, andpeaks labeled with primed stars correspond to a phosphopeptide artifactwith a mass of M-78. These artifacts are also present in the unpurifiedpeptide mix (FIG. 2) but are obscured by the peaks fromnonphosphorylated peptides (M-80).

FIG. 4—depicts a MALDI-TOF mass spectrum of the purified and unpurifiedphosphotyrosine peptide mix described in FIG. 2, usingalpha-cyano-4-hydroxycinnamic acid as matrix. The top panel shows thepeptide mix before purification (as in FIG. 2), and the bottom panelshows the peptide mix after purification (FIG. 3).

FIG. 5—depicts a MALDI-TOF mass spectrum of an unpurified mixture of 4different phosphorylated and nonphosphorylated peptides, usingalpha-cyano-4-hydroxycinnamic acid as matrix. Peaks labeled with starsare phosphorylated peptides, and peaks labeled with circles correspondto nonphosphorylated peptides. Unmarked peaks are synthetic peptidebyproducts.

FIG. 6—depicts a MALDI-TOF mass spectrum of the bound and unboundpeptide fractions after immunoaffinity isolation/purification of thephosphothreonine peptide mix described in FIG. 5, usingalpha-cyano-4-hydroxycinnamic acid as matrix. The top panel shows thefraction of the peptide mix that did not bind to a polyclonalP-Thr-antibody-resin, and the bottom panel shows the fraction of thepeptide mix that did bind to and was eluted from the polyclonalP-Thr-antibody-resin. Peaks labeled with stars are phosphorylatedpeptides, and peaks labeled with circles correspond to nonphosphorylatedpeptides.

FIG. 7—depicts a MALDI-TOF mass spectrum of the unpurified and purifiedphosphotyrosine peptide mix described in FIG. 2, usingalpha-cyano-4-hydroxycinnamic acid as matrix. This isolation is similarto the one described in FIGS. 2-4, except that the amount ofphosphotyrosine peptide mix was reduced to a low level. In all panels,peaks labeled with stars are phosphorylated peptides, peaks labeled withcircles correspond to nonphosphorylated peptides, and peaks labeled withprimed stars correspond to a phosphopeptide artifact with a mass ofM-78. The top panel shows the unpurified, complex phosphotyrosinepeptide mix. The second panel shows the peptides that did not bind tothe monoclonal P-Tyr-100 antibody-resin, and the third panel shows thepeptides that did bind and elute from the antibody-resin. The bottompanel shows the bound and eluted peptide fraction after treatment with aphosphatase enzyme, to remove phosphate groups from phosphopeptides,reducing the observed mass by 80. Lines drawn between the third paneland the bottom panel show the relationships between phosphopeptides anddephosphorylated phosphopeptides.

FIG. 8—depicts a MALDI-TOF mass spectrum of the unpurified and purifiedphospho-Akt substrate peptide mix, using alpha-cyano-4-hydroxycinnamicacid as matrix. Peaks labeled with stars are phosphorylated peptides,peaks labeled with circles correspond to nonphosphorylated peptides, andpeaks labeled with squares are metastable-decomposition phosphopeptideproducts. The top panel shows the peptide mix before purification andthe bottom panel shows the peptide mix after purification.

FIG. 9—depicts a MALDI-TOF mass spectrum of the unpurified and purified14-3-3 binding motif peptide mix, using alpha-cyano-4-hydroxycinnamicacid as matrix. Peaks labeled with stars are phosphorylated peptides,peaks labeled with circles correspond to nonphosphorylated peptides, andpeaks labeled with squares are metastable-decomposition phosphopeptideproducts. Peaks labeled with filled stars are phosphopeptides that arenot expected to bind to the 14-3-3 binding motif antibody because theirsequences do not fit the antibody's known specificity. The top panelshows the peptide mix before purification and the bottom panel shows thepeptide mix after purification.

FIG. 10—depicts a MALDI-TOF mass spectrum of the peptides purified byimmobilized P-Tyr-100 antibody from a mixture containing a digestedcrude 3T3 cell extract, the phosphotyrosine peptide mix, and thephospho-Akt substrate peptide mix, using alpha-cyano-4-hydroxycinnamicacid as matrix (top panel). Peaks labeled with stars are phosphorylatedpeptides. The bottom panel shows the bound and eluted peptide fractionafter treatment with a phosphatase enzyme, to remove phosphate groupsfrom phosphopeptides, reducing the observed mass by 80. Arrows drawnbetween the top panel and the bottom panel show the relationshipsbetween phosphopeptides and dephosphorylated phosphopeptides.

FIG. 11—depicts a MALDI-TOF mass spectrum of the peptides purified byimmobilized phospho-Akt substrate antibody from a mixture containing adigested crude 3T3 cell extract, the phosphotyrosine peptide mix, andthe phospho-Akt substrate peptide mix, usingalpha-cyano-4-hydroxycinnamic acid as matrix (top panel). Peaks labeledwith stars are phosphorylated peptides, and peaks labeled with squaresare metastable-decomposition phosphopeptide products. The bottom panelshows the bound and eluted peptide fraction after treatment with aphosphatase enzyme, to remove phosphate groups from phosphopeptides,reducing the observed mass by 80. Arrows drawn between the top panel andthe bottom panel show the relationships between phosphopeptides anddephosphorylated phosphopeptides.

FIG. 12—depicts a MALDI-TOF mass spectrum of the peptides purified byimmobilized 14-3-3 binding motif antibody from a mixture containing adigested crude 3T3 cell extract and the 14-3-3 binding motif peptidemix, using alpha-cyano-4-hydroxycinnamic acid as matrix. The top panelshows the peptide mix before purification, and the middle panel showsthe peptide mix after purification. Peaks labeled with stars arephosphorylated peptides, peaks labeled with circles correspond tononphosphorylated peptides, and peaks labeled with squares aremetastable-decomposition phosphopeptide products. The bottom panel showsthe bound and eluted peptide fraction after treatment with a phosphataseenzyme, to remove phosphate groups from phosphopeptides, reducing theobserved mass by 80.

FIG. 13—depicts a Western blot of A431 cells overexpressing theepidermal growth factor receptor (EGFR) and probed with P-Tyr-100antibody. Induction of EGFR expression is shown by the major band thatappears after treating the cells with EGF.

FIG. 14—depicts a MALDI-TOF mass spectrum of modified peptides(phosphotyrosine) isolated from an A431 cell extract with P-Tyr-100antibody-resin, using alpha-cyano-4-hydroxycinnamic acid as matrix. Thiscell line overexpresses the EGF receptor and was treated with EGF toinduce phosphorylation at specific sites in the EGF receptor, as shownin FIG. 13. Peaks labeled with stars are phosphopeptides, and peakslabeled with circles correspond to nonphosphorylated peptides.Phosphopeptides purified from the digested lysate with P-Tyr-100antibody-resin corresponded to two known major phosphorylation sites inthe EGF receptor, as expected (top panel). The fraction was treated withphosphatase and reanalyzed (bottom panel) to confirm isolation ofphosphopeptides. Lines drawn between the top and bottom panels indicatethe relationships between phosphopeptides and dephosphorylatedphosphopeptides.

FIG. 15—depicts a Western blot of 3T3 cells stably transfected toexpress active Src protein kinase constituitively and probed withP-Tyr-100 antibody. Comparison to untransfected cells shows the effectof Src expression on the number and level of proteins recognized by theP-Tyr-100 antibody.

FIG. 16—depicts a MALDI-TOF mass spectrum of modified peptides isolatedfrom an extract of 3T3 cells transfected with Src protein kinase (asshown in FIG. 15) with immobilized P-Tyr-100 antibody, usingalpha-cyano-4-hydroxycinnamic acid as matrix (top panel). Peaks labeledwith stars are phosphorylated peptides, and peaks labeled with circlescorrespond to nonphosphorylated peptides. This bound-and-eluted peptidefraction was treated with phosphatase and reanalyzed (bottom panel) toconfirm isolation of phosphopeptides.

FIG. 17—depicts an LC-MS/MS spectrum of one of the modified peptidespurified from an extract of 3T3 cells transfected with Src proteinkinase (as shown in FIG. 15) with immobilized P-Tyr-100 antibody.Portions of the spectrum were amplified to show low-intensity productions. Sequest assigned this particular spectrum to aphosphotyrosine-peptide from enolase A. The peptide sequence andpertinent Sequest scores are shown. Peaks labeled “b” indicate productions that contain the amino-terminus of the peptide, and “y” indicatesproduct ions that contain the carboxyl-terminus. The number followingthe “b” or “y” label indicates the number of peptide residues in thation. Doubly-protonated ions, i.e., ions with a charge (z) of 2, arelabeled “++”.

FIG. 18—depicts a Western blot of Jurkat cells treated with TPA andprobed with phospho-(Ser) PKC substrate antibody. Comparison tountreated cells shows the effect of TPA treatment on the number andlevel of proteins recognized by the phospho-PKC substrate antibody.

FIG. 19—depicts a MALDI-TOF mass spectrum of modified peptides isolatedfrom a TPA-treated Jurkat cell extract (as shown in FIG. 18) withimmobilized phospho-PKC substrate motif antibody, usingalpha-cyano-4-hydroxycinnamic acid as matrix (top panel). Peaks labeledwith stars are phosphorylated peptides, peaks labeled with circlescorrespond to nonphosphorylated peptides, and peaks labeled with squaresare metastable-decomposition phosphopeptide products. Thisbound-and-eluted peptide fraction was treated with phosphatase andreanalyzed (bottom panel) to confirm isolation of phosphopeptides.

FIG. 20—depicts various chromatograms obtained by LC-MS/MS analysis ofthe modified peptides purified from a TPA-treated Jurkat cell extract(as shown in FIG. 18) with immobilized phospho-PKC substrate motifantibody. The top panel shows where survey MS scans were collected (they-axis value is the height of the tallest peak in each individualspectrum), and the second panel shows where MS/MS spectra were collected(the y-axis value is the sum of the heights of all peaks in eachindividual spectrum). The third, fourth, and fifth panels show whereneutral loss of 49, 32.7, and 24.5, respectively, was detected (they-axis value is the height of the neutral-loss ion). The peaks in eachchromatogram are labeled with their corresponding spectrum numbers.

FIG. 21—depicts properties of the peptides that were observed to undergoneutral-loss during the LC-MS/MS analysis shown in FIG. 20, such asmass, phosphate content, and correspondence to peaks in the MALDI-TOFmass spectrum shown in FIG. 19.

FIG. 22—depicts some of the MS/MS spectra (left panels) and MS³ spectra(right panels) acquired during LC-MS³ analysis of the modified peptidespurified from a TPA-treated Jurkat cell extract (as shown in FIG. 18)with immobilized phospho-PKC substrate motif antibody. Each MS³ spectrumis grouped with its corresponding MS/MS spectrum, which caused thedata-dependent MS³ spectrum to be acquired. Sequest was able to assignparent proteins with good confidence to the three MS³ spectra shown.

FIG. 23—depicts the MS/MS spectra (left panels) and MS³ spectra (rightpanels) that confirm an assignment made by Sequest to one of the spectrain FIG. 22. The top panels show the spectra collected for a biologicalpeptide and assigned by Sequest to UFD1_HUMAN residues 333-343 withphosphoserine at residue 335. The bottom panels are the spectracollected for a peptide that was synthesized with this sequence andphosphorylation site. The close correspondence of the biological peptidespectra and the synthetic peptide spectra confirms the assignment madeby Sequest. Portions of the MS/MS spectra were amplified to showweak-intensity product ions.

FIG. 24—depicts a Western blot of 3T3 cells stably transfected toexpress active Akt protein kinase constituitively and treated with PDGF.The extract was analyzed by SDS-PAGE, blotted, and probed, usinguntransfected, untreated cells as a negative control. The top panel isprobed with a general Akt antibody, the second panel with an antibodyspecific for phosphorylation at Akt residue Thr308, and the third panelwith an antibody specific for phosphorylation at Akt residue Ser 473.The bottom panel is probed with phospho-(Ser/Thr) Akt substrate motifantibody. This shows that activation of Akt protein kinase isaccompanied by an increase in the number and level of proteinsrecognized by the phospho-Akt substrate antibody. Other blottingexperiments showed the major protein recognized by the phospho-Aktsubstrate antibody is the ribosomal protein S6.

FIG. 25—depicts a MALDI-TOF mass spectrum of modified peptides purifiedfrom an extract of 3T3 cells transfected with Akt protein kinase andtreated with PDGF (as shown in FIG. 24), usingalpha-cyano-4-hydroxycinnamic acid as matrix (top panel). Immobilizedphospho-(Ser/Thr) Akt substrate motif antibody was used to purifymodified peptides from the digested extract. Peaks labeled with starsare phosphorylated peptides, peaks labeled with circles correspond tononphosphorylated peptides, and peaks labeled with squares aremetastable-decomposition phosphopeptide products. All fourphosphopeptides in the top panel are accompanied bymetastable-decomposition products arising from neutral loss ofphosphate. Two of these fit the expected masses for phosphopeptides fromthe ribosomal protein S6 (2,254.5 and 2,334.4). This fraction wastreated with phosphatase and reanalyzed (bottom panel) to confirmisolation of phosphopeptides. Lines drawn between the top and bottompanels indicate the relationships between phosphopeptides anddephosphorylated phosphopeptides.

FIG. 26—depicts various chromatograms obtained by LC-MS/MS analysis ofthe modified peptides purified from a PDGF-treated 3T3 cell extract (asshown in FIG. 24) with immobilized phospho-(Ser/Thr) Akt substrate motifantibody. The top panel shows where survey MS scans were collected (they-axis value is the height of the tallest peak in each individualspectrum), and the second panel shows where MS/MS spectra were collected(the y-axis value is the sum of the heights of all peaks in eachindividual spectrum). The third, fourth, and fifth panels show whereneutral loss of 49, 32.7, and 24.5, respectively, was detected (they-axis value is the height of the neutral-loss ion). The peaks in eachchromatogram are labeled with their corresponding spectrum numbers.

FIG. 27—depicts properties of the peptides that were observed to undergoneutral-loss during the LC-MS/MS analysis shown in FIG. 26, such asmass, phosphate content, and correspondence to peaks in the MALDI-TOFmass spectrum shown in FIG. 25.

FIG. 28—depicts three MS/MS spectra acquired during the LC-MS/MSanalysis shown in FIG. 26. These three spectra have been tentativelyassigned to the multiply phosphorylated peptide from the ribosomalprotein S6 with one (panel 1), two (panel 2), or three (panel 3)phosphate groups. Neutral loss of one, two, or three phosphate groups isreadily apparent.

FIG. 29—depicts a Western blot of COS-1 cells treated with insulin andan analog of cAMP and probed with phospho-(Ser) 14-3-3 binding motifantibody. Comparison to untreated cells shows the effect of treatment onthe number and level of proteins recognized by the phospho-(Ser) 14-3-3binding motif antibody.

FIG. 30—depicts a MALDI-TOF mass spectrum of modified peptides isolatedfrom a treated COS-1 cell extract (as shown in FIG. 29) with immobilizedphospho-(Ser) 14-3-3 binding motif antibody, usingalpha-cyano-4-hydroxycinnamic acid as matrix (top panel). Peaks labeledwith stars are phosphorylated peptides, peaks labeled with circlescorrespond to nonphosphorylated peptides, and peaks labeled with squaresare metastable-decomposition phosphopeptide products.

FIG. 31—depicts various chromatograms obtained by LC-MS/MS analysis ofthe modified peptides purified from a treated COS-1 cell extract (asshown in FIG. 29) with immobilized phospho-(Ser) 14-3-3 binding motifantibody. The top panel shows where survey MS scans were collected (they-axis value is the height of the tallest peak in each individualspectrum), and the second panel shows where MS/MS spectra were collected(the y-axis value is the sum of the heights of all peaks in eachindividual spectrum). The third, fourth, and fifth panels show whereneutral loss of 49, 32.7, and 24.5, respectively, was detected (they-axis value is the height of the neutral-loss ion). The peaks in eachchromatogram are labeled with their corresponding spectrum numbers.

FIG. 32—depicts properties of the peptides that were observed to undergoneutral-loss during the LC-MS/MS analysis shown in FIG. 31, such asmass, phosphate content, and correspondence to peaks in the MALDI-TOFmass spectrum shown in FIG. 30.

FIG. 33—depicts two MS/MS spectra acquired during the LC-MS/MS analysisof two different samples, one prepared with phospho-(Ser/Thr) Aktsubstrate motif antibody (FIG. 26) (left panels of this figure), theother prepared with phospho-(Ser) 14-3-3 binding motif antibody (FIG.31) (right panels of this figure). In addition to prominent neutral-lossions, the spectra have another prominent product ion in common. Thesespectra are thought to correspond to peptides that are present in bothsamples, due to similar induction conditions and to overlapping motifsrecognized by the antibodies used for purification.

FIG. 34—depicts an LC-MS/MS spectrum of one of the modified peptidespurified from a treated COS-1 cell extract (as shown in FIG. 29) withimmobilized phospho-(Ser) 14-3-3 binding motif antibody. Portions of thespectrum were amplified to show low-intensity product ions. Sequestassigned this particular spectrum to a phosphoserine-peptide from heatshock 27 kDa protein. The peptide sequence and pertinent Sequest scoresare shown. Peaks labeled “b” indicate product ions that contain theamino-terminus of the peptide, and “y” indicates product ions thatcontain the carboxyl-terminus. The number following the “b” or “y” labelindicates the number of peptide residues in that ion. Doubly-protonatedions, i.e., ions with a charge (z) of 2, are labeled “++”.

DETAILED DESCRIPTION OF THE INVENTION

In accordance with the present invention, there is provided a generalmethod for isolating a modified peptide (derived from apost-translationally modified protein) from a complex mixture ofpeptides, such as a digested cell lysate. In general, the methodcomprises the steps of: (a) obtaining a proteinaceous preparation froman organism, the protein preparation comprising modified peptides fromtwo or more different proteins; (b) contacting the proteinaceouspreparation with at least one immobilized modification-specificantibody; and (c) isolating at least one modified peptide specificallybound by the immobilized antibody in step (b). In a preferredembodiment, the method further comprises the step of (d) characterizingmodified peptide(s) isolated in step (c) by mass spectrometry (MS),tandem mass spectrometry (MS-MS), and/or MS³ analysis, or otherequivalent method.

In another preferred embodiment, the invention provides a method forisolating a phosphopeptide from a complex mixture of peptides, themethod comprising the steps of: (a) obtaining a proteinaceouspreparation from an organism, wherein the proteinaceous preparationcomprises phosphopeptides from two or more different proteins; (b)contacting the proteinaceous preparation with at least one immobilizedmotif-specific, context-independent antibody that binds a motifcomprising at least one phosphorylated amino acid; (c) isolating atleast one phosphopeptide specifically bound by the immobilized antibodyin step (b); and (d) characterizing said modified peptide isolated instep (c) by mass spectrometry (MS), tandem mass spectrometry (MS-MS),and/or MS³ analysis. In a preferred embodiment, step (a) furthercomprises digesting said proteinaceous preparation to produce a complexmixture of peptides. In another preferred embodiment, the motif of step(b) comprises all or part of a kinase consensus substrate motif or aprotein-protein binding motif, or consists of a single phosphorylatedamino acid.

In some preferred embodiments, the methods further comprise the step of(e) utilizing a search program to substantially match the spectraobtained for the isolated, modified peptide during the characterizationof step (d) with the spectra for a known peptide sequence, therebyidentifying the parent protein(s) of said modified peptide. In otherpreferred embodiments, the method further includes a quantification stepemploying, e.g. SILAC or AQUA, to quantify isolated peptides in order tocompare peptide levels to a baseline or control state.

The method of the invention enables the single-step isolation (andsubsequent characterization) of multiple different modified peptides,corresponding to a multitude of different modified proteins andsignaling pathways, with a single antibody. The method is, therefore,suitable for genome-wide (e.g. cell-wide or organism-wide) profiling ofactivation states, and is readily automatable. The method allows, forexample, the rapid, cell-wide profiling of modification states, such asphosphorylation, of many different proteins in a test cell or fluid(e.g. a diseased cell) as compared to a reference cell or fluid (e.g. anormal fluid from a healthy organism).

Motif-specific, context-independent antibodies may be advantageouslyemployed in the disclosed methods. These antibodies bind short, modifiedmotifs comprising one or more amino acids including at least onemodified residue in a manner that is highly independent of the differingprotein context in which the motif occurs in multiple signaling proteinswithin a genome. Motif-specific, context-independent antibodies, theirproduction, and their applications are described in U.S. Ser. No.09/148,712, Comb et al. (WO 00/14536). Genome-wide profiling of proteinsusing motif-specific, context-independent antibodies is generallydescribed.

The isolation method of the present invention represents a significantadvance over conventional methods for identifying modification sites inproteins, particularly with respect to the following:

-   -   (i) the method is useful for biological samples that have not        been, or cannot be, radioactively labeled;    -   (ii) complex mixtures of peptides can be resolved in a        single-step and there is no need for timely and costly        purification before analysis;    -   (iii) the method utilizes affinity-chromatography and thus is        more specific than existing methods, such as IMAC, since only        modified peptides are purified, and unmodified peptides do not        contaminate the purified, modified peptide fraction, even when        the overall level of protein phosphorylation is very low;    -   (iv) the method specifically isolates the type of modified        residue targeted by the affinity purification, thus, from one        complex, unpurified mixture, the method can be used to isolate        predefined, non-overlapping subsets of modified peptides (e.g.        phosphotyrosine-containing peptides can be purified using a        general protein modification antibody for phosphotyrosine,        etc.);    -   (v) since the method is based on a stable antibody-antigen        interaction, it does not have to be adjusted as different        samples are analyzed;    -   (vi) the recognized problem with existing protein isolation        methods of having non-specific peptides or proteins binding to,        and co-eluting with, bound modified proteins is obviated since        peptides, not proteins, are purified; accordingly, the present        method eliminates the background associated with the        non-specific co-isolation of proteins other than the desired        modified protein; and    -   (vii) the method is simpler and easier to use than existing        methods, and is, therefore, particularly well-suited to        high-throughput automation and reproduction.

As used herein, the following terms have the meanings indicated:

-   -   “peptide” means a fragment of a whole protein, e.g. a protease        cleavage fragment, having a sequence two or more amino acids        long;    -   “modified peptide” means a peptide having an amino acid sequence        comprising at least one, but alternatively more than one,        post-translationally-modified amino acid, for example (but not        limited to), a phosphorylated amino acid such as        phosphotyrosine, phosphoserine, or phosphothreonine, or an        acetylated amino acid, such as acetyl-lysine; modified peptides        may contain multiple modified residues of the same type (e.g.        two or more phosphorylated residues) or may contain multiple        modified residues of differing type (e.g. a phosphorylated        residue and a glycosylated residue);    -   “complex mixture of peptides” means a substantially unpurified        mixture of a plurality of different peptides corresponding to        two or more different parent proteins, typically including both        modified and unmodified peptides;    -   “proteinaceous preparation” means a preparation of proteins        and/or peptides from one or more cells, tissues, or biological        fluids of an organism, whether unpurified or purified (e.g. IMAC        pre-purified), for example a crude cell extract, a proteolytic        digest, serum, and the like;    -   “antibody” means a natural or recombinant antibody, polyclonal        or monoclonal, derivative or fragment thereof, including F_(ab),        F_(ab′), F(ab)₂ and F(v) fragments;    -   “modification-specific antibody” means an antibody that binds at        least one modified amino acid, either alone or as part of a        modified motif comprising multiple amino acids, including a        general modification-specific antibody or a motif-specific,        context-independent antibody;    -   “general modification-specific antibody” means an antibody that        specifically binds a single modified amino acid, for example a        general phosphotyrosine-specific antibody or a general        acetyl-lysine specific antibody; the term includes, but is not        limited to, a motif-specific, context-independent antibody that        binds a motif consisting of a single modified amino acid;    -   “motif-specific, context-independent antibody” means an antibody        that specifically recognizes a short amino acid motif (typically        comprising 1 to 6 invariant amino acids) comprising at least one        modified amino acid in a manner that is highly independent of        the amino acid sequence surrounding (flanking) the motif in the        peptide (i.e. it recognizes the modified motif in many, if not        most, peptides in which it occurs), but does not substantially        recognize peptides containing the unmodified form of the motif;        (the production of such antibodies, which recognize a plurality        of peptides or proteins within a genome that contain the target        motif, has been previously described in Comb et al., WO        00/14536, supra.); the antibody may bind a motif consisting of a        single modified amino acid or a motif comprising multiple amino        acids including at least one modified amino acid (e.g. all or        part of a kinase consensus substrate motif);    -   “parent protein” means the protein(s) from which a given peptide        is (or potentially is) derived;    -   “phosphopeptide” means a peptide comprising at least one, but        alternatively more than one, phosphorylated amino acid; and

“protein-protein binding motif” means a short, modified motif thatmediates signal transduction protein binding to a target protein, forexample, 14-3-3 binding motifs, PDK1 docking motifs, SH2 domains,phosphotyrosine binding domains, and the like.

The teachings of all references cited in this specification are herebyincorporated herein by reference. Further aspects, advantages and usesof the invention are described in more detail below.

Proteinaceous Preparations

Proteinaceous preparations containing complex mixtures of peptides forisolation of modified peptides according to the method of the inventionmay be obtained from any desired organism. For example, the preparationmay be obtained from bacteria, yeast, worms, amphibia, fish, plants,parasites, insects, or mammals. In a preferred embodiment, the organismis a mammal. In another preferred embodiment, the mammal is a human. Themethod can be applied to a proteinaceous preparation from one or morecell types or fluid samples derived from any organism. Proteinaceouspreparations may be obtained, for example, by growing cells in tissueculture according to standard methods, harvesting the cells from culturemedia by centrifugation, and lysing the cells by sonication or otherstandard means of disrupting cells.

Proteinaceous preparations may also be obtained directly from tissuesamples. In a preferred embodiment, the tissue sample is a biopsysample. These small pieces of living tissue, typically weighing lessthan 500 milligrams, are taken directly from an organism and useddirectly without growth in tissue culture. The use of such living tissueallows direct analysis of the biological state of the tissue withoutintroducing artifacts that may arise as a consequence of growth inculture. Any desired cell type from a given organism may be utilized.For example, tumor cells (e.g. from breast, prostate, etc.) may becultured or obtained by biopsy to study proteins with roles in cancer.Neural cells lines are available to characterize proteins involved inneurotransmission. Fat cells can be cultured or obtained by biopsy tostudy proteins involved in the hormonal mechanisms of fat deposition.Proteinaceous preparations from tissue samples may contain peptides orproteins from multiple cell lines or types. In addition, cell lines withspecific, desirable features could be engineered genetically, e.g., tooverexpress a protein thought to have an important regulatory role in aspecific pathway, e.g. cell lines overexpressing Akt protein. In otherpreferred embodiments, proteinaceous preparations are obtained frombodily fluids, such as serum, urine, spinal fluid, or synovial fluid.Preparations from blood samples may also be employed, whether cells,e.g. erythrocytes, are first removed or not.

Proteinaceous preparations are obtained by standard methods, e.g. forcells and tissues, by sonication, homogenization, abrasion, enzymaticdigestion, or chemical solubilization. Generally the method used to lysecells will be the one most commonly used for that specific cell type,e.g., enzymatic lysis for bacteria, abrasion for plant cells, andsonication for animal cells, but other desired methods may be suitablyemployed. Proteinaceous preparations for use in the method of theinvention need not be extensively purified prior to the immunoaffinityisolation step. For example, urine samples or serum samples may bedirectly analyzed. This allows less sample processing, which increasesthe likelihood of identifying low-level modifications and makes it lesslikely that fractionation methods will bias or skew the profile ofexperimentally assigned modifications.

The mixture can be a crude cell lysate (for example, from tissueculture, a biopsy, or serum), a partially fractionated lysate (forexample, a highly purified membrane or organelle), or a known andwell-defined composition (for example, an in vitro modificationreaction, that is, a protein modification enzyme allowed to react withone or more substrate proteins). However, if desired, simplepurifications may be carried out to remove non-protein elements and/ornon-signaling, structural proteins by standard methods, e.g. bycentrifugation to remove erythrocytes, ultracentrifugation to removecellular debris and cytoskeletal proteins, or by treatment withclass-specific enzymes such as nucleases to remove DNA and RNA. In apreferred embodiment, the proteinaceous preparation is a crude cellextract or fluid, which has not been extensively purified.

Preferably, proteinaceous preparations are obtained so as to reflect thebaseline, in vivo activation state, e.g. phosphorylation state, ofproteins in a given cell, e.g. a breast cancer cell. However,proteinaceous preparations may be obtained from cells or organismspre-treated with inducers. For example, cells grown in tissue culturecan be exposed to chemicals such as calyculin or okadaic acid, whichbroadly elevate cellular phosphoprotein levels by inhibiting cellularphosphatases. Alternatively, a considerably narrower and more specificset of phosphoproteins in pathways can be induced by treatment withhormones, such as epidermal growth factor, that activate certainsignaling pathways. Organisms can also be treated with drugs orinfectious agents, and the effects of these treatments can be evaluatedby isolating and analyzing specific tissues or fluids from the organism.

To obtain a complex mixture of peptides, the proteinaceous preparation,which contains a great variety of different proteins, is digested with asuitable proteolytic enzyme, e.g. trypsin or chemical cleavage reagent.Any suitable enzyme that yields a significantly digested proteinaceouspreparation (i.e. mostly peptides as opposed to proteins) may beemployed, for example endoproteinases Lys-C, Glu-C, Asp-N, chymotrypsin,and thermolysin. In a preferred embodiment, the enzyme is trypsin. Ifdesired, digestion with two or more different proteolytic enzymes may becarried out to yield smaller peptides suitable for mass spectrometryanalysis (e.g., peptides of about 30 amino acids in length or less, forcurrent MS methods). Digestion of proteins may be carried out in anenzymatic solution or with immobilized proteolytic enzymes (e.g.trypsin-POROS resin, available from Applied Biosystems, Inc.,Framingham, Mass.; trypsin-Matrix F7m, available from MoBiTec, MarcoIsland, FL.), which can easily be removed from the digest bycentrifugation or filtration before the preparation is contacted withthe immobilized antibody. If soluble proteolytic enzymes are used, thedigests are preferably treated with inhibitors such as PMSF oralpha-2-macroglobulin before the proteinaceous preparation is contactedwith the immunoaffinity purification device, so that the proteolyticenzyme will not degrade the immobilized antibody molecules.Alternatively, soluble proteolytic enzymes are removed byprefractionating peptides by solid phase extraction prior to contactwith the immobilized antibody. Digestions are conducted for a period oftime sufficient for complete digestion, that is, for cleavage of allpeptide bonds that can be cleaved by the protease. However, if thedigestion is incomplete, intentionally or not, the overlap betweenpartially digested peptides can provide further evidence that thephosphorylation site has been assigned correctly, i.e., when the samephosphorylation site is found in more than one peptide because thepeptides overlap due to incomplete digestion, the site assignment ismore convincing. In a preferred embodiment, a protease that can cleaveat a large variety of residues, e.g., chymotrypsin, thermolysin, orelastase, is used for digestion in a manner that deliberately generatespeptides with overlapping sequences.

Preferably, proteinaceous preparations for use in the method of theinvention contain modified peptides, e.g. phosphopeptides, from two ormore different proteins, and in most cases contain modified peptidesfrom a multitude of different proteins. The proteinaceous preparationtypically contains a complex mixture of many different types ofmodified, as well as unmodified, peptides. For example, such mixturesmay contain peptides modified by phosphorylation, acetylation,methylation, sulfation, nitrosylation, or glycosylation, among others.See, e.g. Krishna et al., Adv. Enzymol. Relat. Areas Mol. Biol. 67:265-98 (1993); Parekh et al., Curr. Opin. Biotechnol. 8: 718-23 (1997).

In a preferred embodiment, the proteinaceous preparation containsphosphopeptides from two or more different proteins. Accordingly, thesecomplex mixtures of modified peptides reflect the activation state, e.g.phosphorylation state, of signaling pathways in a given organism or celltype on a genome-wide or cell-wide basis, thus providing a snap-shot ofactivation states in that organism. The complex mixture of modifiedpeptides in the proteinaceous preparation reflects the baseline, in vivoactivation status in the given organism or cell line, but may, asdiscussed above, reflect activation status in a treated cell, so as toreflect the effect of treatment upon activation status.

In certain preferred embodiments, the proteinaceous preparationcomprises a digested biological sample selected from the groupconsisting of a digested crude cell extract, a digested tissue sample, adigested serum sample, a digested blood sample, a digested urine sample,a digested synovial fluid sample, and a digested spinal fluid sample.The digested preparation may be obtained using at least one proteolyticenzyme, such as trypsin. In a preferred embodiment, the proteolyticenzyme is immobilized. In another preferred embodiment, the proteolyticenzyme is soluble, and the said digested preparation is treated with aproteolysis inhibitor prior to the contacting step (b).

In one preferred embodiment the method is coupled with quantitative massspectrometry approaches, so that modified peptides are identified and atthe same time their levels in the sample are measured. The absence of amodified peptide is more meaningful when quantitative mass spectrometryapproaches are used, because that peptide has been sought and not found,as opposed to overlooked. In addition, modified peptides that arepresent in two samples may be present at very different levels, but thisdifference is not easily recognized in qualitative identificationstudies, even though it may be a key feature of the system beingstudied. SILAC (stable isotope labeling by amino acids in cell culture)can be used for relative quantification of two cell culture samples,e.g., a cell line treated with a drug can be compared to the same cellline left untreated. See, e.g. Ong et al., Mol. Cell. Proteomics 5:376-86 (2002). Another quantitative mass spectrometry strategy is termedAqua for absolute quantification. See Gerber, Rush et al. Proc. Natl.Acad. Sci. U.S.A. 100: 6940-5 (2003). In Aqua a sample is compared to apanel of synthetic peptide standards, which serve as a referencecontrol. Unlike SILAC, Aqua is better suited for the development ofassays based on mass spectrometry, and it can be applied to tissuesamples as well as cell cultures.

Immunoaffinity Isolation

The proteinaceous preparation, which contains a complex mixture ofmodified and unmodified peptides from a plurality of different proteins,is contacted with an immobilized, modification-specific antibody (e.g.anti-phosphothreonine) in order to isolate many, if not most, peptidescontaining the modification for which the immobilized antibody isspecific. Peptides with the appropriate modification bind to theimmobilized antibody, while unmodified peptides and/or peptides withother modifications do not. Thus, immunoaffinity purification accordingto the disclosed method allows the one-step isolation of a broad rangeof desired peptides (originating from different proteins) fromsubstantially unpurified, complex mixtures of peptides.

In a preferred embodiment, the antibodies are covalently-linked to aninert chromatography resin, such as agarose, polystyrene, or silica, bystandard techniques. Briefly, the carbohydrate groups of the antibodymolecules are oxidized to reactive aldehyde groups, which are thencovalently bonded to the hydrazide groups of derivatized chromatographyresins. See, e.g. Hoffman et al., J. Immunol. Methods 9:113-120 (1988).The carbohydrate groups of the antibody are not required for antigenrecognition, so the chemical modification does not interfere with theirability to bind peptides. Using this standard method or others,antibodies are attached to chromatography supports at highconcentrations, and because the antibodies are attached covalently tothe resin, they do not leach off the support and contaminate purifiedsamples. Alternatively antibodies may be immobilized by non-covalentattachment to protein A or protein G, which have been previouslycovalently linked to agarose resin, as in another preferred embodiment.It is simpler to immobilize antibodies to protein A- or proteinG-agarose than it is to covalently immobilize antibodies to agarose.However antibodies immobilized to protein A or protein G supports havethe disadvantage that they can be used only once, because theinteraction of the antibody with protein A or protein G is disrupted bythe conditions used to elute peptides from the antibody. When thecomplex mixture of peptides in the proteinaceous preparation iscontacted with the antibody-resin, in either batch or column format, theantibody-resin selectively binds the modified peptides, even when theyare present at low levels (i.e. picomole amounts).

For example, in batch format, the proteinaceous preparation is contactedwith the antibody-resin by mixing as a slurry, and the antibody-resinwith bound peptides is then removed by centrifugation, filtration, etc.Alternatively, in column format, the covalently-linked antibody-resin iscontained within/packed in a chromatography column, and theproteinaceous preparation is passed through the column, so peptides thatare recognized by the immobilized antibody are retained on the columnand unrecognized peptides pass through the column. The antibody-resinmay, in another preferred embodiment, be contained within a micropipettetip.

Column size, flow rates, and conditions (e.g. pH, choice of buffer) areselected in accordance with standard techniques. For low-level samples,a substance such as BSA, detergent, or polymer may be added to theproteinaceous preparation prior to contact with the immobilized antibodyin order to prevent non-specific peptide loss through adsorption. Theimmunoaffinity purification step may be optimized, if desired, to ensurethat all modified peptides in the sample are quantitatively bound to andeluted from the antibody-resin (i.e. little, if any, desired modifiedpeptide is unbound). For example, the molar ratio of antibody tomodified peptides, the amount of antibody per unit mass ofantibody-resin, the length of time the sample contacts theantibody-resin (including recirculating the sample through anantibody-resin column), the temperature at which contact occurs, theinclusion of additives (e.g., salts, detergents, organic solvents, orpolymers) that may enhance interaction of modified peptides with theantibody-resin, etc., may, if desired, each be optimized by the skilledartisan in practicing the method of the invention. Generally the metricfor evaluating optimization is maximizing the number of modifiedpeptides observed during analysis, with some emphasis given tominimizing the number of unmodified peptides that are isolated, which isa measure of the specificity of the method for modified peptides. Thiscan be evaluated by MALDI-TOF mass spectrometry, before and aftertreatment with phosphatase, an enzyme that removes phosphate frompeptides and lowers the measured masses of phosphopeptides. It can alsobe evaluated by the actual peptide sequences determined by tandem massspectrometry. Other optimizations are possible, e.g., reducing theamount of time needed to analyze a sample without reducing the number ofmodified peptides identified and increasing the number of modifiedpeptides identified by using different types of separation systems ormass spectrometers for analysis, e.g., capillary electrophoresis forseparating peptides instead of reversed-phase HPLC, orquadrupole-time-of-flight hybrid mass spectrometry instead of ion trapmass spectrometry for analysis.

In a preferred embodiment, immunoaffinity isolation is carried out byutilizing a device consisting of one or more modification-specificantibodies immobilized to a rigid, non-porous or macroporous resinparticle, packed into a thin capillary column, with an internal diameterof about 50 to 300 micrometers. While capillary columns of this typecontaining reversed-phase or ion exchange supports are already widelyused, prior to the instant invention, capillary columns packed withimmunoaffinity supports, as disclosed herein, have not been described.Immunoaffinity isolation devices of the invention may be constructed ofany suitable material, for example, fused silica capillaries. The endsof the capillaries are drawn to fine tips, so the internal diameter atthe tip is 3 micrometers or less, using an electronic microcapillarypuller. The capillaries are then packed with chromatography resin usinga Jorgensson and Kennedy pressure bomb, to force the resin slurry intothe column through the back end. See Gatlin et al. Anal. Biochem. 263:93-101 (1998). Resin particles are larger than the diameter of thecapillary tip, so the resin accumulates in the column and is packed bypressure applied through the bomb. When the packed column has reachedthe desired length, the pressure is relieved, the empty back of thecapillary is trimmed away, and the column is stored or used.

A preferred resin is POROS, a rigid macroporous resin developed atPerseptive Biosystems for use in perfusion chromatography. Resinparticles are about 20 micrometers in diameter and are of uniform size.The resin is sold commercially through Applied Biosystems (Framingham,Mass.), including chemically derivatized resins for covalently attachingproteins such as antibodies. Other suitable types of resins known tothose of skill in the art may be employed, for exampled, magneticDynaBeads from Dynal.

This immunoaffinity isolation column can be adapted to be used as (i.e.coupled to) part of an electrospray source on a mass spectrometer, sothat peptides can be readily analyzed after isolation with minimalsample loss. The capillary column itself is fitted directly to the massspectrometer and acts as a fritless electrospray interface. For example,using standard low-volume HPLC fittings, the column is inserted into aplastic (PEEK) micro-tee fitting (shaped like the letter T). A capillaryline from the HPLC solvent delivery system is attached to the oppositeside of the micro-tee fitting, in line with the column, so differentsolvents or a gradient of solvents can be delivered at low flow rates,typical less than 1 microliter/minute, through the column to elutesamples bound to the column. A gold rod is inserted into the third stemof the micro-tee, perpendicular to the solvent delivery lines andcolumn, to supply the electrical connection from the mass spectrometerthrough a liquid-metal junction. All three devices are secured in thefitting with standard PEEK micro-fingertight fittings and tubingsleeves. The source normally used with the mass spectrometer is removedand replaced by a metal platform that holds this micro-tee assembly. Theposition of the capillary column tip can be precisely controlled bymaking adjustments with an XYZ micromanipulator on the platform, so theposition of the spraying column tip relative to the mass spectrometerorifice is optimized for maximum ion current signal. In this waymicrocolumn liquid chromatography and micro-electrospray ionization maybe combined into one device.

The solutions used to elute bound samples from immunoaffinity columns,e.g., 30% acetic acid or 0.1 M glycine, pH 2.3, typically are notcompatible with direct analysis by electrospray mass spectrometry.However, the immunoaffinity purification device can be used as the firstcomponent of a two-dimensional HPLC system, where an immunoaffinitypurification column and a reversed-phase column are directly connected.A two-dimensional HPLC system using a strong cation exchange columnupstream of a reversed phase column has been described. See, e.g.Washburn et al. Nat. Biotech. 19: 242-247 (2001).

The liquid stream from the HPLC system is diverted to waste during theimmunoaffinity purification step. As samples elute from theimmunoaffinity purification column, they bind to the downstreamreversed-phase capillary column, but the solution components used forelution do not bind and are diverted to waste. The bound samples canthen be eluted from the reversed-phase column using solvents that arecompatible with direct analysis by electrospray mass spectrometry.Alternatively, the immunoaffinity step can be done off-line, using asolid-phase extraction cartridge in a micropipette tip, as describedbelow, and then applied to a reversed-phase capillary column in anLC-MS/MS system. In both cases, the capillary columns are mounted in themass spectrometer and samples are ionized as they elute from the columnas described in Gatlin, supra.

Immunoaffinity isolation devices comprising capillary columns asdescribed herein are useful not only for peptides that bind and elutefrom the column, but also for peptides that bind to the antibodies withlower affinity and whose passage through the column is retarded,extending the usefulness of the method. These columns would be reusableand have lifetimes comparable to other types of capillary HPLC columns.See, e.g. Gatlin, supra.

In another preferred embodiment, the immunoaffinity isolation device isa solid-phase extraction cartridge in a micropipette tip. Devices thathave been constructed with reversed-phase and other types of HPLCsupports (e.g., ZipTips from Millipore) have been described. See e.g.,Erdjument-Bromage et al, J. Chromatogr. A 826:167-181 (1998). Thesedevices are attached to standard laboratory pipetting devices and areused in the same manner as pipette tips: as the sample is aspirated intothe tip, it becomes bound to the chromatography support, which is thenwashed before eluting the sample in a small volume for analysis. Thetip, for example, may be fabricated by embedding immobilizedantibody-resin in a gel matrix in the dispensing end of a standardmicropipette tip. See, e.g. Chirica et al., Anal. Chem. 72: 3605-3610(2000). Taking advantage of the general stability of antibody molecules,these devices may be supplied dry; the end user would then rehydrate andcondition the gel containing immobilized antibody immediately beforeuse. These high-capacity, small-volume tips would be used to fractionate(i.e. isolating desired peptide) one sample and then discarded.Immunoaffinity separation may also be performed with other types ofsolid supports, such as porous filtration membranes or sample supportsfor MALDI-TOF mass spectrometry. See, e.g. Weller, Fresenius J. Anal.Chem. 366: 635-645 (2000); Liang et al. Anal. Chem. 70: 498-503 (1998).

Immunoaffinity isolation according to the method of the invention may becarried out without additional chromatography steps (e.g.,reversed-phase or ion exchange chromatography). However, in somepreferred embodiments, additional chromatography methods may be employedin conjunction with, and prior to, the single-step immunoaffinityisolation of the present method. For example, a digested cell lysate canbe applied to a reversed-phase solid-phase extraction cartridge andfractionated by increasing the organic solvent concentration as thecartridge is washed in steps. Each fraction would thus be enriched forcertain peptides, with minimal overlap between fractions, and thefractionated peptides could be more concentrated than the peptides inthe unfractionated digested cell lysate. In the same manner, thedigested cell lysate could be prefractionated with an ion-exchangesolid-phase extraction cartridge, which would be developed by washingthe cartridge in steps with increasing concentrations of salt.

In one preferred embodiment of the method, immobilized metal affinitychromatography (IMAC) is employed as an upstreampre-purification/fractionation step prior to immunoaffinity isolation asdisclosed herein. As discussed earlier, although IMAC can enrichphosphopeptides from peptide mixtures, it has several importantlimitations (such as purification of phosphopeptides without specificityfor the particular phosphorylated residue, purification of acidicpeptides that are not phosphorylated, incomplete purification ofphosphopeptides (i.e., some peptides do not bind or elute from the IMACsupport), and poor reproducibility (which makes it difficult to comparesamples)) which render it unsuitable for the selective and facileisolation of phosphopeptides from complex mixtures. Despite itslimitations as a stand-alone technology, however, IMAC may be desirablyemployed as a bulk phosphopeptide enrichment/pre-purification stepupstream of the method of the present invention.

For example, IMAC may be performed at very low stringency, in order tobind as many phosphopeptides as possible without regard for the muchlarger number of acidic non-phosphopeptides that would also bind to theIMAC support under these conditions. After elution from the IMAC column,the peptides would be fractionated further by the method of theinvention, which would separate acidic non-phosphopeptides fromphosphopeptides and which would further separate phosphopeptides intodiscrete subsets based on the particular residue that is phosphorylated.For example, peptides that contain phosphotyrosine and peptides thatcontain the Akt substrate binding motif would be separated from eachother and could be isolated from the same IMAC-prepurified digested celllysate. Thus the method of the invention may be desirably practiced inconjunction with other methods of phosphopeptide purification.

In another preferred embodiment, the method of the invention is usedwith several non-overlapping modification-specific antibodies in seriesto extract well-defined, distinct modified peptide populations from asingle sample. For example, peptides containing phosphotyrosine arefirst extracted from a digested cell extract using immobilizedphosphotyrosine antibody; the digested extract is then separated fromthe phosphotyrosine antibody-resin and treated with a second immobilizedantibody, e.g., phosphothreonine-proline antibody, to extractphosphopeptides containing phosphothreonine-proline motifs. Thisprocess, which we have termed “rational fractionation” or “modifiedpeptide sorting”, can be repeated for as many steps as there arenon-overlapping modification-specific antibodies. When each group ofextracted, modified peptides is analyzed by mass spectrometry,identification of modified sites is simpler than for modified peptidesthat have been purified in bulk because the majority of peptides in eachgroup are highly likely to contain a predetermined modification, e.g.,phosphotyrosine or phosphothreonine-proline. With this strategy, samplecomplexity is addressed before analysis rather than after analysis,resulting in a larger number of high-confidence identifications.

Modification-Specific Antibodies

In accordance with the invention, immunoaffinity isolation is carriedout by using at least one modification-specific antibody thatspecifically recognizes a given type of post-translational modification,e.g. phosphorylation, acetylation, methylation, nitrosylation,glycosylation, etc. Preferably, the modification-specific antibody is:(i) a general modification-specific antibody, that is, an antibody thatbinds a single modified amino acid residue, e.g. phosphothreonine, butdoes not recognize the unmodified amino acid residue, and/or (ii) amotif-specific, context-independent antibody produced by the methoddescribed in Comb et al., WO 00/14536, supra (also described below).Motif-specific, context-independent antibodies against many differentphosphorylated kinase consensus substrate motifs and protein-proteinbinding motifs are commercially available. (See CELL SIGNALINGTECHNOLOGY, INC. 2003-04 Catalogue & Technical Reference, pages 12-24).

The use of such modification-specific antibodies (both general and/ormotif-specific, context-independent) thus allows the single-stepisolation of many, if not most, peptides in a complex mixture thatcontain the modification or motif, regardless of the peptide sequencesurrounding the modification or motif (i.e. these antibodies are not“site-specific” and hence are not limited to recognition of particularlonger peptide sequences presenting a uniquely-occurring site epitope).

In a preferred embodiment of the method, the modification (on thepeptides to be isolated) comprises phosphorylation and the modifiedpeptide(s) isolated comprise(s) a phosphopeptide. Particularly preferredphosphorylated residues are phosphotyrosine, phosphoserine,phosphothreonine, or phosphohistidine. Although the invention isdemonstrated in the Examples using phospho-specific antibodies, it willbe recognized by those of skill in the art that othermodification-specific antibodies may be readily employed, for example,acetylation-specific antibodies. Virtually any desired modified peptidemay be isolated, as described in “Proteinaceous Preparations” above.

In certain preferred embodiments, motif-specific, context-independentantibodies are advantageously employed in the disclosed method toisolate many, if not most, peptides containing a desired modified motif.These antibodies and their production have previously been described.See Comb et al., WO 00/14536, supra. The antibodies bind to short,modified motifs, which, because of their small size and degeneratesequences, occur more than once in a given genome (i.e. occur in two ormore different proteins, as opposed to larger, unique epitopes or“sites” that statistically occur only once) and thus serve,biologically, as consensus sequences and conserved binding sites for,e.g. kinases, in multiple proteins in cellular signaling pathways.

The invention may utilize antibodies specific for any desired motif ofinterest, e.g. signaling pathway motifs, comprising one or more modifiedamino acids. In certain preferred embodiments of the disclosed method,the modification-specific antibody used to isolate peptides comprises amotif-specific, context-independent antibody that recognizes a motifcomprising at least one phosphorylated amino acid. In one preferredembodiment, the motif consists of a single phosphorylated amino acid,such as phosphotyrosine, phosphothreonine, or phosphoserine. In anotherpreferred embodiment, the motif comprises all or part of a kinaseconsensus substrate motif or a protein-protein binding motif.

For example, in preferred embodiments, motif antibodies specific for allor part of any of the following kinase consensus or protein-proteinbinding motifs are used for immunoaffinity isolation: MAPK consensussubstrate motifs, CDK consensus substrate motifs, PKA consensussubstrate motifs, AKT consensus substrate motifs, PKC consensussubstrate motifs, PDK1 docking motif (bulky ring),phosphothreonine-X-arginine, ATM/ATR consensus substrate motifs, 14-3-3binding motifs, p85 PI3K binding motif, phosphothreonine-proline motif,Arg-X-Tyr/Phe-X-phosphoserine motif, andphosphoserine/phosphothreonine-Phe motif. (See, e,g. CELL SIGNALINGTECHNOLOGY 2003-04 Catalogue at p.14). Context-independent antibodiesagainst any desired kinase consensus substrate motif or protein-proteinbinding motif may be advantageously employed in the method of theinvention; such motifs are well described in the literature (see, e.g.,Kemp et al., Trends in Biochem. Sci. 15:342-46 (1990); Kemp et al.,Methods in Enzymology 200: 62-81 (1991); al-Obeidi et al., Biopolymers47:197-223 (1998); see also L. Cantley, overview in Cell SignalingTechnology, Inc. 2000-2001 Catalogue at p. 198.)

The preparation of motif-specific, context-independent antibodies,previously described in Comb et al., WO 00/14536, supra (the disclosureof which are incorporated by reference in their entirety) is carried outbriefly as follows:

-   -   (1) Motif-specific antibodies that react with any protein or        peptide containing specific target residues independently of the        surrounding amino acids may be obtained by synthesizing a highly        degenerate peptide library. In one preferred embodiment, the        library comprises XXXXXXJ*XXXXXXC where X=all 20 amino acids        except cysteine and J*=a modified (*) amino acid (J). It will be        appreciated that a shorter or longer library may be generated        and less than all of the surrounding amino acids may be varied.        For example, one to four X residues may be selectively biased        for 1 or 2 specific amino acids, while the remaining X residues        are highly degenerate. In one preferred embodiment, the peptide        library is about 6 to 14 residues long. While one preferred        embodiment utilizes one fixed amino acid (either modified or        unmodified) in a varied surrounding context, other preferred        embodiments may utilize a motif comprising several fixed amino        acids. Likewise, the surrounding sequence of the library may be        varied at more than one position simultaneously, or, as in the        preferred embodiment, varied at only one surrounding sequence        position per degenerate molecule, such that a library is        produced which is completely degenerate at every position except        the fixed residue(s). The peptide library can be synthesized by        standard Fmoc solid phase peptide synthesis using an ABI peptide        synthesizer and using mixtures of each amino acid during        degenerate coupling reactions.    -   The incorporation of unmodified amino acids at fixed positions        may be selected to mimic conserved motifs, for example zinc        fingers or repeating arginine residues.    -   (2) In order to produce as equal a representation of each amino        acid as possible at each degenerate position, several rounds of        altering the amino acid composition, synthesizing, and peptide        sequencing are conducted. Amino acid sequence analysis at        several different positions along the peptide is conducted to        verify a random amino acid representation at each position and        that the random representation is maintained throughout the        synthesis. It will be recognized by one of skill in the art that        the number of rounds may vary in order to achieve an equal        distribution of all amino acids at each position.    -   (3) The highly diverse peptide library is used as an antigen,        preferably by covalent coupling to a carrier. In a preferred        embodiment, keyhole limpet hemocyanin (KLH) emulsified in        Freund's adjuvant is used as the coupling agent, and the coupled        peptide library injected intradermally into a host, such as        female New Zealand white rabbits. Booster injections may be        given in incomplete Freund's adjuvant until an immune response        is obtained. Antibody titer is measured by a suitable method,        such as ELISA against the motif-specific peptide libraries.        Antisera raised in this manner may be used in either crude or        purified preparations, as outlined below.    -   (4) Antisera from the most promising hosts are purified, for        example over protein A, and adsorbed over a J (non-modified)        peptide library column. In the preferred embodiment, the        nonadsorbed fraction (flow through) is then applied to a J*        column, eluted at suitable pH, dialyzed and tested for J*        specificity by a suitable method, such as ELISA using J* and J        as antigen.    -   (5) Antibodies affinity purified in this fashion recognize the        J* peptide library but do not react with the J library and        exhibit a high degree of specificity for J*. These antibodies        may be further tested for lack of reactivity against the        unmodified form of the target modified amino acid, J*, or a J*        homologue, utilizing a suitable method, such as ELISA.    -   (6) Antibodies may be further tested by western blotting, or        another suitable method, using cell extracts prepared from cells        treated with and without a selected protein modification enzyme        inhibitor, such as protein phosphatase inhibitor okadaic acid.        Treatments that increase protein modification will increase the        number of antibody reactive proteins as well as the intensity of        reactivity. The J* specific antibodies will react with a        relatively small number of proteins from control extracts but        will react with a very large number following treatment. The        antibodies will show no reactivity with the        inactive-non-modified versions of these proteins, demonstrating        a high degree of J* specificity and suggesting broad        cross-reactivity to many different modified-target containing        proteins.    -   (7) The degree of context-independence may be more carefully        examined, for example, by ELISA analysis against individual J*        peptides that are mixed together or tested individually. Such        analysis can indicate if poor reactivity occurs with certain        motifs, such as when J* is followed by proline, for example.    -   (8) The context-dependence of J* antibody recognition may be        further examined using an immobilized grid of modified-peptide        libraries. In addition to a fixed target residue, J*, each        different library is synthesized to contain an additional fixed        amino acid at different positions relative to J* but with all        other positions containing all 20 amino acids except cysteine.        Each peptide library is coated, for example, on the bottom of an        ELISA well and exposed to the J* antibodies. Antibodies that do        not react with a particular spot (peptide library) on the grid        do not bind when the specified amino acid is present at the        specified position. This analysis determines whether or not a        particular amino acid at a particular position relative to J*        will allow or block binding.    -   Alternatively, purified antibodies can be linked to resin,        allowed to bind the modified or unmodified library, unbound        sequences washed away, and bound sequences recovered and subject        to amino acid sequencing to determine the amount of each amino        acid present at each position in the library. This information        will indicate what amino acids are tolerated at each position.

Antibodies suitable for use in the method of the present invention maybe polyclonal or monoclonal, or may be a fragment thereof, e.g. an Fabfragment, or a derivative thereof, e.g. a humanized antibody. A singleantibody, e.g. a general phosphothreonine antibody, may be used in theimmunoaffinity step, or two or more antibodies may be simultaneouslyused to isolate peptides containing different modifications, e.g.acetylated lysine and phosphothreonine. Alternatively, isolation ofpeptides with one modification may first be carried out with oneimmobilized antibody, and then peptides with other modifications maysubsequently be purified using other immobilized antibodies and/orresins. This process, which we have termed “rational fractionation” or“modified peptide sorting”, can be repeated for as many steps as thereare non-overlapping modification-specific antibodies.

Following contact with the immobilized antibody, the antibody/resin isthoroughly washed to remove unbound peptides and then peptides bound tothe antibody/resin (i.e. those containing the desired modification) areisolated from the resin by eluting with a small volume of an acidicsolution, e.g. 30% acetic acid, or other suitable eluting solution. Theeluted peptides are analyzed directly as described below, orconcentrated and desalted with a micropipette tip containingreversed-phase resin, and then analyzed. If desired, peptide sequenceand/or parent protein information is obtained by mass spectroscopy.

In certain circumstances, analysis of purified peptides (as describedbelow) may indicate that some undesired peptides that lack the targetmotif are co-purified along with peptides that contain the desiredtarget motif. In such cases, the number or stringency of the resinwashes may be increased to eliminate non-specific peptide binding.Stringency of washes may be increased according to techniques well knownin the art, for example, by including additives that reduce backgroundbinding, such as detergents, organic solvents, or polymers.

Analysis of Isolated Peptides

Isolated peptides containing the desired modification may be analyzed bystandard methods to determine peptide sequence, activation state, andmass. In certain preferred embodiments, modified peptides isolatedaccording to the method of the invention are analyzed by massspectrometry (MS) methods, since MS is presently the most sensitivemethod for analyzing peptides. MS requires less analyte material toprovide high-quality information about peptides than other currentmethods. It will be recognized by the skilled artisan that equivalent orsubsequently improved methods of analyzing modified peptides are withinthe scope of the invention. For example, at present, peptides of about30 amino acids in length or less are most suitable for MS analysis, butfuture improvements in methods may allow the analysis of longerpeptides.

Accordingly, in a preferred embodiment, the general method of theinvention further comprises the step of (d) characterizing the modifiedpeptide(s) isolated in step (c) by mass spectrometry (MS), tandem massspectrometry (MS-MS), and/or MS³ analysis. In one preferred embodiment,matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)mass spectrometry is utilized to measure the masses of purifiedpeptides. MALDI-TOF mass spectrometry is useful for rapidly screeningsamples before analyzing them by other, more complex methods such astandem mass spectrometry (MS/MS)(see below), and is both sensitive andsimple. For proof-of-principle experiments or diagnostic assays, wherethe objective of the isolation is to determine if an expected peptide ispresent among the purified modified peptides, the mass of the purifiedpeptide(s) is calculated from the peptide's known sequence and searchedfor in the mass spectrum.

MALDI-TOF mass analysis of peptides is a rapidly evolving field, and thepreferred methods for preparing isolated modified peptides for analysisand carrying out such analysis is likely to change over time.Nonetheless, MALDI-TOF analysis is carried out according to standardmethods (see, e.g. Courchesne et al., Methods in Mol. Biol. 112:487-511(1999)), and improvements in these methods are within the scope of thepresent invention. For example, isolated peptides are prepared forMALDI-TOF analysis using only a small portion, 1 to 20%, of the isolated(purified) modified peptide-containing fraction, and analyzed by mixingdirectly with a equal volume of saturated matrix solution, e.g.alpha-cyano-4-hydroxycinnamic acid, and drying the peptide-matrixsolution on the MALDI-TOF sample plate. Other suitable matrix solutionsmay be alternatively employed. If necessary, a larger sample aliquot canbe concentrated and desalted with a micropipette tip containingreversed-phase matrix before mixing it with matrix solution.

To confirm that purified peptides contain the desired modification, asmall portion of the sample is preferably analyzed before and aftertreatment with an enzyme that removes the modified group from thepeptide. For example, where the modified peptides being purified arephosphopeptides, phosphate is removed using a suitable phosphatase, e.g.calf intestinal phosphatase. See, e.g. Larsen et al. Proteomics 1:223-238 (2001). This is a simple and reliable assay to confirm thatpeptides are modified, and to count the number of modified groupspresent in each peptide. For example, phosphatase treatment will reducethe observed peptide mass by 80 for each phosphate group in the peptide.The mass of a peptide that is not phosphorylated will not change as aresult of phosphatase treatment. Similarly, any suitablemodification-specific enzyme known in the art may be selected to confirmthat peptides isolated according to the method of the invention containthe desired modification. See e.g., Krishna, supra.

If phosphopeptides are being isolated, metastable decomposition mayresult in the presence of additional peaks in the mass spectrum.Metastable decomposition of phosphopeptides has been noted by others andcan be used to recognize and assign phosphopeptides in a MALDI-TOF massspectrum (Annan and Carr, Anal. Chem. 68: 3413-21 (1996)). The peaks fordecomposition products are broader than the peaks for phosphopeptidesbecause the decomposition products form after ionization and theinstrument is configured to focus ions that are stable during analysis.For similar reasons, the expected mass shift for loss of phosphate is−98, but −84 mass shifts are observed because, unlike a stable ion, themass of a decomposition product changes during analysis. Analysis of alarge number of synthetic phosphopeptides by MALDI-TOF mass spectrometryhas indicated that some peptides containing phosphoserine orphosphothreonine—but not phosphotyrosine—residues undergo metastabledecomposition. Accordingly, metastable decomposition is a reliableindicator of peptides that contain phosphoserine or phosphothreonine.Metastable decomposition may be observed in the MALDI-TOF spectra ofsome peptides that contain phosphoserine or phosphothreonine, withoutadditional sample treatment steps and without consuming more sample.

In other types of applications, for example in a genome-wide analysisemploying the disclosed method, it may not be possible to identify themodified peptides isolated from the complex mixture present in aproteinaceous preparation simply by measuring peptide masses becausemany different peptide sequences could produce each mass observed in theisolated modified peptide fraction. Accordingly, in another preferredembodiment, modified peptides isolated from complex mixtures (e.g. crudecell extracts) are analyzed by tandem mass spectrometry (MS/MS or MS³),where peptide ions isolated in one stage of mass spectrometry aredeliberately fragmented by collisions in the mass spectrometer, and thenthe fragment masses are measured. See, e.g. Yates, Methods in Enzymology271: 351-377 (1996). The fragment masses observed for each peptide are aproperty of that peptide's sequence and are a more specific indicator ofthe parent protein than the peptide's mass, i.e. the fragment masses arerelated to the peptide's sequence and can be used to identify theprotein from which the peptide originated. If the sequence of thepeptide's parent protein is known, then the peptide can be unambiguouslymatched to its parent protein without directly interpreting a sequencefrom the fragment mass spectrum.

A particular peptide's measured mass and partial sequence is sufficientto unambiguously match it to its parent protein. See e.g. Eng et al. J.Am. Soc. Mass Spectrom. 5: 976-989 (1994). Parent protein sequences areincreasingly becoming available as the genomes of common biologicalmodel organisms become known. MS/MS spectra can be collected rapidly(<400 msec per peptide) and in a data-dependent manner throughinstrument-control software, so very complex samples are amenable toanalysis. With nanospray infusion methods, sample volumes of 2microliters can be analyzed for an hour or longer. See e.g. Wilm et al.,Anal. Chem. 68:1-8 (1996). Accordingly, in a preferred embodiment of thedisclosed method, modified peptides isolated in step (c) arecharacterized by tandem MS, for example liquid chromatography (LC)-MS/MS(as described in Example IV).

If phosphopeptides are being isolated, it may be observed that duringthe fragmentation process of MS/MS, peptides containing phosphoserine orphosphothreonine often form an ion by simple loss of phosphate toproduce a neutral-loss ion that has a mass 98 lower than theunfragmented parent ion. If the parent ion has a charge of +1, theneutral-loss ion has a mass-to-charge value (m/z) of 98/1 or 98 lowerthan the parent ion mass-to-charge value. Likewise, phosphopeptideparent ions with charges of +2, +3, or +4 will give neutral-loss ionswith m/z values that are 49, 32.7, and 24.5 lower than the parent ion.

Neutral loss during MS/MS is the same process as metastabledecomposition during MALDI-TOF mass spectrometry. Therefore many of thephosphopeptides showing neutral loss during LC-MS/MS are expected to bethe same phosphopeptides that give metastable decomposition duringMALDI-TOF mass spectrometry. For each neutral-loss MS/MS spectrum, theparent ion mass (m) can be calculated from the parent ion mass-to-chargevalue (m/z) and the charge (z) inferred from the neutral loss value (+2for neutral loss of 49, +3 for 32.7, and +4 for 24.5). Some individualpeptides may be observed to undergo neutral loss as +2, +3, and +4 ions.A comparison of datasets can confirm that the same peptides are detectedby both mass analysis methods.

Additional steps can be incorporated into the method of the invention asneeded to identify modified peptides that give high levels of neutralloss during MS/MS and correspondingly low levels of peptide backgroundfragmentation. One approach is to analyze these peptides with a massspectrometer that uses a different fragmentation mechanism, expectingthis will change the distribution of unproductive neutral-lossfragmentation to productive peptide backbone fragmentation. For example,analysis with ion trap mass spectrometers may exacerbate neutral lossbecause fragmentation is induced by gradually increasing the energy ofthe trapped peptide ion over a relatively long period of time, whereasanalysis with a triple quadrupole mass spectrometer may allow morebackbone fragmentation because the peptide ions become energized forfragmentation more suddenly. A second approach is to chemically treatmodified peptides that have been purified by the method of the inventionin a manner that removes the group that undergoes neutral loss duringMS/MS but leaves a “remnant” indicating where the group was. Forexample, phosphate groups can be removed chemically from phosphopeptidesby beta-elimination. See, e.g., Byford, Biochem J. 280: 261-5 (1991).Exposing the peptides briefly to a base, such as NaOH, LiOH, or Ba(OH)₂,results in the removal of phosphoric acid from phosphoserine andphosphothreonine, leaving dehydroalanine and dehydroaminobutyric acid,respectively, which can be distinguished from serine and threonineresidues in the peptide by mass: residue masses are 69 fordehydroalanine, 87 for serine, 167 for phosphoserine, and 83 fordehydroaminobutyric acid, 101 for threonine, 181 for phosphothreonine.Beta-eliminated peptides can be analyzed by tandem mass spectrometrydirectly or after further reaction with a Michael addition reagent. See,e.g., Molloy and Andrews, Anal Chem. 73: 5387-94 (2001).

Following MS/MS characterization, modified peptides may be unambiguouslyidentified by analyzing the product ion spectra with a search program inan attempt to match the spectra obtained for the modified peptide withthe spectra for a known peptide sequence, thereby identifying the parentprotein(s) of the modified peptide. For example, Sequest, a program thatcorrelates an experimental spectrum to a library of theoretical spectraderived from protein sequence databases to find a best-fit match, mayadvantageously be used for such a search. It will be recognized thatequivalent search programs may be employed in the practice of disclosedmethod. Accordingly, in a preferred embodiment, the method of theinvention further comprises the step of (e) utilizing a search programto substantially match the spectra obtained for the modified peptideduring the characterization of step (d) with the spectra for a knownpeptide sequence, thereby identifying the parent protein(s) of themodified peptide.

In certain cases, if phosphopeptides are being isolated, it may beobserved that, during MS/MS, some phosphopeptides undergo neutral lossto a very high degree, with very little residual fragmentation along thepeptide backbone (which is needed to produce spectra of a quality highenough for unambiguous assignments). In such cases, analysis of MS/MSproduct ion spectra using a search program (such as Sequest) in anattempt to assign a phosphorylation site and parent protein to eachpeptide may not result in unambiguous assignments. This is a commonlimitation encountered during MS/MS analysis of peptides containingphosphoserine and phosphothreonine. See e.g., DeGnore et al., J. Am.Soc. Mass Spectrom. 9: 1175-1188 (1998). Even when phosphopeptides losephosphate by neutral loss, the position of the phosphorylation site canbe determined, as long as there is sufficient residual backbonefragmentation, because neutral loss leaves an unusual residue at thephosphorylation site: phosphoserine becomes dehydroalanine, andphosphothreonine becomes dehydroaminobutyric acid.

Accordingly, in a preferred embodiment of the disclosed method, isolatedmodified peptides may be further characterized by MS³ (for exampleLC-MS³, as in a preferred embodiment) analysis; that is, theneutral-loss ions may be subjected to an additional level of MS to givesufficient backbone fragmentation for identification. This process issimpler to implement on ion trap mass spectrometers than on other typesof mass spectrometers. As peptides elute from the LC system, a survey MSscan is performed, and MS/MS spectra are collected for the three mostabundant ions, if they are above a pre-set intensity threshold and ifthey have not been recently analyzed by MS/MS already. However, ifneutral loss of 49, 32.7, or 24.5 is detected during MS/MS, then beforecollecting another MS/MS spectrum or another survey MS scan, theinstrument first isolates the neutral loss ion, fragments it, andmeasures the product ion masses. In the case of phosphopeptides, if theneutral-loss ion no longer contains phosphate, it is more likely tofragment like a non-phosphorylated peptide and give a useful product ionspectrum. With certain modifications to the instrument control software,MS³ spectra can be collected in the same data-dependent manner as MS/MSspectra, and the MS³ spectra can be analyzed further with Sequest. SeeTomaino and Rush et al. Abstract ThOE 3:00, presented at the 50^(th)ASMS Conference on Mass Spectrometry and Allied Topics, Jun. 6, 2002.

Following MS³ analysis, peptides may again be identified using a searchprogram such as Sequest. In the event that a given peptide isunambiguously identified but the program is unable to distinguishbetween multiple possible phosphorylation sites, the most likelyphosphorylation site may be chosen by comparing the sites to the knownspecificity of the modification-specific antibody used in the isolation.For example, two possible phosphorylation sites (encompassing Ser 585and Ser 588 of PTN6_HUMAN) were distinguished by noting that thesequence context of one possible site but not the other fits the knownspecificity of the phospho-(Ser) PKC substrate motif antibody used toisolate the peptide (see Example V).

In cases where peptides comprising multiple modification sites areisolated, it may be difficult to obtain unambiguous assignments becauseof the high level of neutral loss with very little residualfragmentation along the peptide backbone. At present, for example,multiply-phosphorylated peptides cannot be analyzed effectively byLC-MS³ using the currently available version of Sequest software. Thecurrent data-dependent acquisition software isolates and fragments themost abundant neutral-loss ion; for multiply phosphorylated peptidesthis corresponds to the peptide with one phosphate removed by neutralloss, leaving one or more phosphate groups to undergo neutral lossduring MS³. However, the acquisition software is being revised (perpersonal communication) to recognize multiples of neutral loss and toisolate and fragment the ion with the highest level of neutral loss,even if it is not the most intense product ion. It is expected,therefore, that further analysis of multiply-modified peptides withrevised acquisition software will allow the parent proteins andmodification sites of some of these peptides to be assigned.Accordingly, the scope of the present invention includes such futurerevisions and versions of acquisition software, such as Sequest.

Following assignment of a peptide sequence and phosphorylation site to aspectrum, the assignment may be confirmed by establishing that asynthetic peptide with that sequence and phosphorylation site gives thesame spectrum. This establishes a formal link between a specificphosphopeptide and its spectrum. This is a simple and convincing way tofurther evaluate marginal Sequest assignments, for example, or toconfirm assignments that are considered especially important.

A simple confirmation method is essential to strategies that attempt toassign phosphorylation sites globally, such as the method of theinvention. Neutral loss of phosphate from phosphoserine orphosphothreonine can make it difficult to assign a peptide sequence toan MS/MS spectrum and occasionally assignments will be ambiguous. Incontrast to global methods, when analyzing a single phosphorylatedprotein, e.g., isolated as a stained band by SDS-PAGE, thenon-phosphorylated peptides from the protein will be available foranalysis and will help to identify the protein, making assignment ofphosphopeptides simpler, because the set of possibilities can berestricted to peptides that originate from that identified proteininstead of a much larger database of proteins. However, in a globalproteomic method, such as the method disclosed herein, where, forexample, phosphopeptides are isolated and analyzed separately fromnon-phosphorylated peptides, often the only peptide from a particularprotein will be the isolated phosphopeptide, and unambiguous assignmentsare likely to be more difficult to achieve. Assignments that are notunambiguous can be confirmed by synthesizing a peptide with the assignedsequence and phosphorylation site and analyzing it by LC-MS/MS or LC-MS³to determine whether it produces the same spectrum as the biologicalpeptide.

As described above, the tendency of some phosphopeptides to undergomoderate to excessive neutral loss of phosphate can make it difficult toassign a sequence to the spectrum of a particular phosphopeptide.Programs such as Sequest provide a ranked list of assignments for eachspectrum. For non-phosphorylated peptides the top-ranked assignment madeby Sequest is often correct, but for phosphopeptides the correctassignment may not have the highest rank because of the additionalcomplexities in the spectrum due to neutral loss and the inability ofSequest to recognize and take into account these neutral loss peaks.However a unique feature and advantage to antibody-based isolationmethods, such as the present invention, is that the known specificity ofthe antibody can be used to screen marginal assignments, i.e.,assignments that are not top-ranked, to find ones worth pursuingfurther. That is, antibody-based isolation methods have an inherentadvantage over other isolation methods because the antibody'sspecificity can be used to partially compensate for some of thelimitations associated with MS/MS analysis of phosphopeptides.

As discussed above, in practicing the immunoaffinity isolation methodsof the invention, a device for isolating modified peptides from theproteinaceous preparation may be coupled directly to a mass spectrometerso that peptides are analyzed as they elute from theimmunoaffinity-isolation device, enabling the mass spectrometer toanalyze even more complex mixtures of peptides. For example, a liquidchromatography system fractionates complex peptide mixtures into simplermixtures, which are then analyzed immediately by the mass spectrometerwithout intervening sample-handling steps. In this manner, the method ofthe invention may be readily automated, so as to allow the efficient,high-throughput isolation of modified peptides from complex mixtures.

To increase the tolerance for complex samples even further, the liquidchromatography system may be multi-modal, i.e. it can operate in two ormore separation modes sequentially. For example, one set of modifiedpeptides may be eluted from an ion-exchange support onto areversed-phase support, followed by a reversed-phase separation into themass spectrometer, and then another set of modified peptides may beanalyzed by a more potent elution from the ion-exchange support onto thereversed-phase support and a second reversed-phase separation into themass spectrometer, and so forth, iteratively. See, e.g. Washburn, supra.

It is also contemplated that one dimension of multi-modal liquidchromatography could be immunoaffinity purification, using generalmodification-specific antibodies to purify post-translationally modifiedpeptides, as described herein. In this sense the immunoaffinity columnwould resemble a so-called enzyme reactor column, a column ofimmobilized protein used upstream of a mass spectrometer to catalyze areaction on the sample to be analyzed. See e.g. Amankwa et al. ProteinSci. 4: 113-125 (1995).

Identification of Novel Sites; Antibodies

The immunoaffinity isolation methods of the invention allow theefficient and rapid isolation and identification of peptides comprisingprotein modification sites from complex mixtures. Modified peptidesisolated according to the method of the invention may comprise knownmodification sites on a particular protein, or may comprise novel sitesof modification previously unreported. For example, unknownphosphorylation sites of a particular protein may be identified inaccordance with the method of the present invention. Similarly, themethods of the invention may isolate and identify sites whosemodification (e.g. phosphorylation) is known, per se, but whosemodification in a particular cell, tissue, disease state, etc. is notknown. Thus, the disclosed methods enable, in part, the identificationof modification sites of particular proteins that are relevant (i.e. theproteins are activated or de-activated) to a particular disease state.

The identification of novel protein modification sites enables thegeneration of new antibody reagents which are specific for the novelprotein site in its phosphorylated form. For example, the identificationof a novel phosphorylation site (e.g. a particular phosphoserine site)according to the method of the invention enables the generation ofphospho-specific antibodies which bind to that protein only whenphosphorylated at the novel site. If a motif-specific,context-independent antibody is employed for the immunoaffinityisolation, novel sites identified will match the specificity of themotif-antibody employed. These modification-specific antibodies againstnovel sites will be highly useful reagents for the detection of proteinmodification, as well as for diagnostic or therapeutic uses.

Once a novel modification site is identified, modification-specificantibodies to that site may be generated by standard techniques familiarto those of skill in the art. The antibodies may be polyclonal ormonoclonal. Anti-peptide antibodies may be prepared by immunizing anappropriate host with a synthetic phospho-peptide antigen comprising thenovel modification site, according to standard methods. See, e.g.,ANTIBODIES: A LABORATORY MANUAL, Chapter 5, p. 75-76, Harlow & LaneEds., Cold Spring Harbor Laboratory (1988); Czernik, Methods InEnzymology, 201: 264-283 (1991); Merrifield, J. Am. Chem. Soc. 85:21-49(1962)). Monoclonal antibodies may be produced in a hybridoma cell lineaccording to the well-known technique of Kohler and Milstein. Nature265:495-97 (1975); Kohler and Milstein, Eur. J. Immunol. 6: 511 (1976);see also, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel et al. Eds.(1989). Motif-specific, context-independent antibodies may also beproduced against the novel site identified if the site is a motifconserved among a plurality of different signaling proteins. See Comb etal., WO 00/14536, supra.

Modification-specific antibodies generated against novel sites and/ormotifs identified by the immunoaffinity methods of the invention may bescreened for epitope and modification-specificity according to standardtechniques. See, e.g. Czernik et al., Methods in Enzymology, 201:264-283 (1991). For example, in the case of a novel phosphorylationsite, the antibodies (whether polyclonal or monoclonal) may be screenedagainst a phospho and non-phospho peptide library by ELISA to ensurespecificity for both the desired antigen (i.e. that epitope includingthe novel phosphorylation site/residue) and for reactivity only with thephosphorylated form of the antigen. Peptide competition assays may becarried out to confirm lack of reactivity with other non-target proteinphosphoepitopes. The antibodies may also be tested by Western blottingagainst cell preparations containing the parent protein, e.g. cell linesover-expressing that protein, to confirm reactivity with the desiredphosphorylated target. Specificity against the desired phosphorylatedepitopes may also be examined by construction of parent/target proteinmutants lacking phosphorylatable residues at positions outside thedesired epitope known to be phosphorylated, or by mutating the desiredphospho-epitope and confirming lack of reactivity.

In accordance with the present invention, two novel proteinphosphorylation sites were identified by the practice of the disclosedimmunoaffinity isolation methods: (i) a novel ubiquitin fusiondegradation protein 1 (UFD1) phosphorylation site (Ser335, comprisingthe sequence GQS*LR) was identified using phospho-(Ser) PKC substratemotif antibody for immunoaffinity isolation of modified peptides from aJurkat cell extract, and (ii) a novel protein-tyrosine phosphatase 1c(PTN6) phosphorylation site (Ser588, comprising the sequence KGS*LK) wasidentified using the same PKC substrate motif antibody forimmunoaffinity isolation of modified peptides from Jurkat cell extracts(see Example V).

Phospho-specific antibodies that bind either UFD1 or PTN6, respectively,only when phosphorylated at these novel sites can now readily beprepared, according to standard techniques. Synthetic phospho-peptideantigens comprising the UFD1 or PTN6 sequence surrounding and includingphospho-Ser335 or Ser588, respectively, may be selected and constructedin accordance with well known techniques, and used as immunogens toproduce poly- or mono-clonal antibodies. See, e.g., ANTIBODIES: ALABORATORY MANUAL, supra, Czernik, Methods In Enzymology, supra. Thephospho- and epitope-specificity of these antibodies may be confirmed asdescribed above.

Accordingly, in a preferred embodiment, the invention also provides anantibody that binds ubiquitin fusion degradation protein 1 (UFD1) onlywhen phosphorylated at serine 335, but does not substantially bind toUFD1 when not phosphorylated at this residue. The UFD1 (pSer335)antibody of the invention also does not substantially bind to proteinsother than UFD1, although some limited cross-reactivity may be observedwith proteins containing sites highly homologous to the UFD1phospho-Ser335 site.

In another preferred embodiment, the invention provides an antibody thatbinds protein-tyrosine phosphatase 1 c (PTN6) only when phosphorylatedat serine 588, but does not substantially bind to PTN6 when notphosphorylated at this residue. The PTN6 (pSer588) antibody of theinvention also does not substantially bind to proteins other than PTN6,although some limited cross-reactivity may be observed with proteinscontaining sites highly homologous to the PTN6 phospho-Ser588 site.

Profiling and Diagnostic Applications

As noted above, the invention enables the rapid, efficient, and directisolation of modified peptides from complex mixtures, such as crude cellextracts or biological fluids, without the need for costly andtime-consuming pre-purification of desired peptides or proteins. Themethod makes possible the single-step immunoaffinity isolation ofmultiple different modified peptides, corresponding to a multitude ofdifferent modified proteins and signaling pathways, with a singleantibody. Accordingly, the methods disclosed herein are suitable andhighly useful for genome-wide (e.g. cell-wide) profiling of activationstates, for example. The simplicity of the disclosed method also makesit readily automatable, as only a single immunoaffinity isolation stepis required.

Facile isolation of modified peptides aids in the identification andassignment of modification sites in a great variety of differentproteins. These protein modifications occur in response to significantevents in the life of a cell, and in some cases the modificationsprovide a potential target for diagnosing or preventing the event. Asthe genome sequences of various organisms continue to become known, theneed to find and assign these modifications in a given organism willbecome even more pronounced. In a broad context, the invention is usefulnot only to assign modification sites in well-defined in vitrocomplexes, but also to generate genome-wide or cell-wideactivation/modification profiles, that is, to determine how globalprotein modification changes within a given cell or tissue in responseto environmental changes, such as stress, inflammation, disease, drugtreatment, etc.

In contrast to conventional proteomics methods, which focus on howglobal protein levels change in response to a particular treatment, thepresent invention focuses on cellular changes in protein modificationresulting from a given event, such as disease or treatment. Proteinmodification, such as phosphorylation and dephosphorylation, serves as amolecular switch for modulating many important biological processes,including cellular transformation and cancer, programmed cell death,cell cycle control, and metabolism. Thus, one advantage offered by thepresent invention is that it provides a means of focusing on thesemolecular switching events, which can occur without an accompanyingchange in the amount of a specific protein in a cell, i.e. a cellularresponse may be triggered by a change in the modification state of aspecific signaling protein, and not by a change in the amount of thatprotein in the cell.

The immunoaffinity isolation methods of the invention will be useful forthe diagnosis of a condition known to be associated with the activation(or de-activation) of a given modification site on a protein. Forexample, a phosphorylation site on a certain cell signaling proteinwhich is a known marker of a given disease may be isolated (from aclinical tissue or fluid sample) in accordance with the invention toidentify the phosphorylation status (i.e. activation status) of themarker in a patient. This marker activation information will assist inthe diagnosis of disease and/or identify subjects at risk of disease.Accordingly, in a preferred embodiment of the disclosed method, themodified peptide isolated in step (c) corresponds to a known marker ofdisease.

The methods of the invention will be useful for profiling proteinactivation (i.e. modification) states in a target cell or fluid, on agenome-wide, or pathway-wide basis, in response to environmental changessuch as disease or drug treatment. For example, biopsy samples may beobtained from cancer patients and analyzed against normal, referencetissue or cells from the same patient. Alternatively, the method will beuseful both for discovering modified protein markers for specific typesof cancer, and as a diagnostic assay for those cancers, perhaps helpingto mark their stage of progression. Accordingly, in one preferredembodiment of the method, the modified peptide(s) characterized in step(d) comprise(s) an unknown modification site of a parent protein. Forexample, the method may be advantageously employed to identifyphosphorylation sites on particular cell signaling proteins that areelevated or reduced in cancerous tissue, as opposed to normal tissue. Ina similar manner, the method will be useful to evaluate the cellulareffects of a therapeutic drug (i.e. changes in protein modification) togauge if it is having the desired effect, or to determine when itsdosage may induce toxicity. For example, cells or tissue treated with atest drug intended to reduce phosphorylation of a particular proteinknown to be associated with a certain disease state may be monitored todetermine the phosphorylation state of that protein and/or others. Themethod could also be used to monitor the stages and severity of aninfectious disease by monitoring changes in cell-wide modification stateduring the course of the disease.

Accordingly, in a preferred embodiment, the isolation method of theinvention further comprises the step of (e) comparing the modificationstate of the modified peptide characterized in step (d) with themodification state of a corresponding peptide in a reference sample,thereby to compare protein activation in the proteinaceous preparationwith protein activation in the reference sample. In one preferredembodiment, the proteinaceous preparation corresponds to a diseasedorganism and the reference sample corresponds to a normal organism,whereby comparison of protein activation provides information onactivation changes resulting from the disease. In a second preferredembodiment, the proteinaceous preparation is obtained from a tissuebiopsy cell or a clinical fluid sample and the reference samplecorresponds to a diseased organism, whereby the comparison of proteinactivation provides information useful for diagnosis of the disease. Ina third preferred embodiment, the protein preparation corresponds withan organism or preparation treated with at least one test compound andthe reference sample corresponds with an untreated organism orpreparation, whereby the comparison of protein activation providesinformation on activation changes resulting from treatment with the testcompound.

In another preferred embodiment, the comparison of protein activationdescribed above identifies the modified peptide characterized in step(d) as corresponding to a parent protein not previously reported as somodified in the disease.

The isolation of modified peptides relevant to a given disease asoutlined above may be carried out for virtually any disease in whichaberrant signal transduction (i.e. protein activation/modification) isinvolved or suspected of being involved. In a preferred embodiment ofthe method, the disease is cancer. Similarly, the modified peptideisolation may be employed to monitor the effects of virtually any testcompound or drug on protein modification. In a preferred embodiment, thetest compound comprises a cancer therapeutic. In a particularlypreferred embodiment, the test compound comprises a kinase inhibitor,such as STI-571 (Gleevac®), an inhibitor of Abl kinase for the treatmentof leukemia.

In the profiling and diagnostic applications described here, theproteinaceous preparation from which modified peptides will be isolatedmay correspond, for example, to a diseased cell or fluid, tissue biopsycell or clinical fluid sample, or test cell treated with a test drug orfluid from an organism treated with a test drug, and the referencesample may correspond to a normal cell or fluid, diseased cell or fluid,or untreated cell or fluid from an untreated organism, whereby theprofiling provides information useful in changes in, e.g. modificationstate, resulting from disease or drug treatment, or diagnosis ofdisease. Alternatively, the reference sample may correspond to a stateof aberrant signaling (i.e. a diseased sample) and the proteinaceouspreparation may correspond to a normal organism, for example, a patientbeing tested for the presence of a marker of disease or susceptibilityto disease.

The isolation and profiling methods of the invention will beparticularly useful in the high-throughput identification ofmodification states on known or unknown proteins on a genome-wide basis,so as to provide a link between genomic and proteomic information andactual disease states. The method is readily automatable, and thus, forexample, may be advantageously employed by pharmaceutical companieswishing to efficiently and rapidly identify markers of disease fordiagnostic or therapeutic applications.

Quantification of Isolated Peptides

In one preferred embodiment the method may employ additional proceduresto allow quantification of modified peptides prepared according to themethod of the invention. For example, in SILAC (stable isotope labelingby amino acids in cell culture) cell cultures are grown in culture mediathat has been depleted of specific amino acids, e.g., arginine andlysine, and then supplemented with these amino acids in “normal isotope”or stable, “heavy isotope” forms. See, e.g. Ong et al., Mol. Cell.Proteomics 5: 376-86 (2002). Cells grown in heavy-isotope media can betreated with a drug candidate that is expected to inhibit one specificprotein kinase, while the same cells grown in normal-isotope media areleft untreated. When these samples are prepared for analysis by themethod of the invention, the cells are harvested and mixed at aone-to-one ratio. In all subsequent steps these two admixed samples arehandled as one sample, so any mass spectrometry intensity differencesbetween the samples can be attributed only to drug treatment and not tosample handling or run-to-run analysis variations. Differences in thesamples are traced to the drug-treated or untreated sample on the basisof the presence or absence, respectively, of the heavy-isotope in theanalyzed peptides during mass spectrometry. SILAC provides relativequantification and is considered to be a promising key method fordiscovering biomarkers by comparative, quantitative mass spectrometry.An alternative method for quantification is Aqua (absolutequantification). See Gerber, Rush et al. Proc. Natl. Acad. Sci. U.S.A.100: 6940-5 (2003). In this method, the modified peptide to bequantified is synthesized as a heavy-isotope peptide, which can thenserve as an internal quantification standard. A known amount of theheavy-isotope peptide is added to the sample prior to digestion with aprotease. Because the heavy-isotope peptide standard is chemicallyidentical to the biologically derived peptide to be quantified, theywill co-purify by the method of the invention and will be mass analyzedat the same time. By multiplying the known amount of heavy-isotopepeptide standard by the measured ratio of biological peptide to peptidestandard, the absolute amount of biological peptide in the sample isdetermined. In contrast to the SILAC method, the Aqua strategy providesabsolute quantification and can be used with a wide variety of sampletypes other than cell cultures. The Aqua method is a preferredembodiment of the method of the invention when it is desirable toquantify a limited number, e.g., 1 to 60, of modified peptides such asin the development of quantitative assays based on mass spectrometry. Akey element of the Aqua strategy is identifying peptides that can bemeasured quantitatively because it is known they can be detected whenanalyzed by mass spectrometry, in contrast to peptides that are selectedby a de novo process and that expected to be present but cannot bedetected. In a preferred embodiment, the method of the invention isfirst used to determine the peptides that are suitable for measurementby the Aqua strategy and then later used as part of an Aqua-based massspectrometry quantification assay. A third method for quantification isbased on chemical modification of peptides with normal-isotope andheavy-isotope chemical modification reagents, e.g., reagents that reactwith peptide amino groups or carboxylic acid groups. See, e.g., Zhang etal. Nat Biotechnol. 21: 660-6 (2003). This follows the same overallstrategy as the SILAC method, except samples are mixed after thechemical modification step and samples other than cell cultures can beanalyzed.

The following Examples are provided only to further illustrate theinvention, and are not intended to limit its scope, except as providedin the claims appended hereto. The present invention encompassesmodifications and variations of the methods taught herein which would beobvious to one of ordinary skill in the art.

EXAMPLE I

A. Isolation of Phosphotyrosine-Containing Peptides from a PeptideMixture

To establish that phosphopeptides can specifically be purified fromcomplex mixtures without contamination from nonphosphorylated peptides,the method of the invention was used to isolate phosphotyrosine(p-Tyr)-containing peptides from a mixture of phosphorylated andnonphosphorylated synthetic peptides. A phosphotyrosine peptide mixcomprising 5 phosphotyrosine-containing peptides and their 5nonphosphorylated partner peptides was prepared (Table 1); note thenonphosphorylated peptides have the same sequences as the phosphorylatedpeptides but are not phosphorylated, that is, they contain tyrosineinstead of phosphotyrosine. Peptides were synthesized by Fmoc chemistryon a Rainin/Protein Technologies Symphony peptide synthesis instrumentand using Fmoc-Tyr(PO(OBzl)OH)—OH as the phosphotyrosine monomer. SeePerich, Lett. Pept. Sci. 6:91 (1999). The peptide mixture covers a broadmass range designed to resemble a protein digest. TABLE 1 Components ofthe Phosphotyrosine Peptide Mix Calculated Protonated Sequence PeptideMass KIEKIGEGTY*GVVYKGRHK 2,242.174 (SEQ ID NO: 1) KIEKIGEGTYGVVYKGRHK2,162.208 (SEQ ID NO: 2) RLIEDNEY*TARQGAKC 1,946.879 (SEQ ID NO: 3)RLIEDNEYTARQGAKC 1,866.912 (SEQ ID NO: 4) LQERRKY*LKHRC 1,709.878 (SEQID NO: 5) LQERRKYLKHRC 1,629.911 (SEQ ID NO: 6) RQGKDY*VGAIPVDC1,600.719 (SEQ ID NO: 7) RQGKDYVGAIPVDC 1,520.752 SEQ ID NO: 8GKDGRGY*VPATC 1,303.550 (SEQ ID NO: 9) GKDGRGYVPATC 1,223.583 (SEQ IDNO: 10)Y* = phosphotyrosineY = tyrosineThe MALDI-TOF mass spectrum of the mixture before immunoaffinitypurification is shown in FIG. 2. Peaks labeled with a star correspond tophosphorylated peptides, and peaks labeled with open circles correspondto the nonphosphorylated partner peptides.

P-Tyr-containing peptides were specifically isolated from the diversepeptide mixture by contacting the phosphotyrosine peptide mix (46 nmoltotal) with a phosphotyrosine monoclonal antibody P-Tyr-100 immobilizedto agarose resin (Cell Signaling Technology, Inc., product number 9419)(100 μl). The antibody was incubated with the peptides as a slurry, in abatch purification format. The slurry was left at room temperature for10 minutes and on ice for 1 hour. The unbound peptides were removed bycentrifugation through a plastic frit, and the retained antibody-resinwas washed extensively (twice with 1 ml of ice-cold phosphate bufferedsaline containing 0.5% NP-40, twice with 1 ml of ice-cold phosphatebuffered saline, and once with water). To elute bound phosphopeptides,the antibody-resin was resuspended in 400 μl 30% acetic acid, left atroom temperature for 10 minutes, and centrifuged. The eluted peptidefraction was dried and resuspended in 80 μl water (the volume of thephosphotyrosine peptide mix before treatment with antibody-resin), and a1 μl aliquot was diluted and analyzed by MALDI-TOF mass spectrometry, asdescribed above (FIG. 3). FIG. 4 shows the mass spectrum of thephosphotyrosine peptide mix before (top panel) and after (bottom panel)immunoaffinity purification. Note that the fraction eluted from theantibody-resin contains all 5 phosphopeptides but none of thenonphosphorylated peptide partners. Accordingly, the method of theinvention specifically isolates all desired phosphopeptides containing aphosphotyrosine, regardless of the different sequences in which thephosphotyrosine occurs, from a complex mixture of phosphorylated andnonphosphorylated peptides.

B. Isolation of Phosphothreonine-Containing Peptides from a PeptideMixture

The method of the invention was further demonstrated using a secondgeneral protein modification antibody, a phosphothreonine polyclonalantibody P-Thr-polyclonal to purify peptides containing phosphothreoninefrom a mixture of phosphorylated and nonphosphorylated syntheticpeptides. The mixture consists of 4 synthetic peptides: 2phosphothreonine-containing peptides and their 2 nonphosphorylatedpartner peptides (see Table 2). The MALDI-TOF mass spectrum, obtained asdescribed above, of the phosphothreonine peptide mix beforeimmunoaffinity purification according to the invention is shown in FIG.5. TABLE 2 Components of the Phosphothreonine Peptide Mix CalculatedProtonated Sequence Peptide Mass DTQIKRNT*FVGTPFC 1,806.825 (SEQ ID NO:11) DTQIKRNTFVGTPFC 1,726.859 (SEQ ID NO: 12) CKEGLGPGDTTST*F 1,491.620(SEQ ID NO: 13) CKEGLGPGDTTSTF 1,411.653 (SEQ ID NO: 14)T* = phosphothreonine,T = threonineA P-Thr-polyclonal antibody (Cell Signaling Technology, Inc., productnumber 9381) was linked to agarose resin using a hydrazide chemistry(the same chemistry used to produce the P-Tyr-100 agarose resin used inExample 1A above), using a commercially available crosslinking kit(BiORad Affi-Gel HZ Immunoaffinity Kit, product number 153-6060) andfollowing the manufacturer's instructions. Each milliliter of resin wasreacted with 1 milligram of antibody. P-Thr-containing phosphopeptideswere specifically isolated from this mixture by contacting thephosphothreonine peptide mix (20 μmol total) with this antibody-resin(100 μl), and incubating the resin and peptides at 4° C. overnight. Theresin was recovered and washed, and the bound peptides were eluted,processed, and analyzed as described above. FIG. 6 shows the MALDI-TOFmass spectra of the unbound and bound peptide fractions. The unboundfraction contains all 4 peptides, including the phosphopeptides; underthe particular conditions utilized, which were not optimized, some ofeach isolated phosphopeptide has passed through the column. The boundfraction contains both phosphopeptides but does not contain thenonphosphorylated peptide partners. Accordingly, the method of theinvention selectively isolates all desired phosphopeptides containing aphosphothreonine, regardless of the different sequences in which thephosphothreonine occurs, from a mixture of phosphorylated andnonphosphorylated peptides.C. Isolation of Phosphotyrosine-Containing Peptides from Low-LevelSamples

The isolation of modified peptides from low-level samples (i.e. wherethe amount of each modified peptide is about 1 μmol or less) accordingto the method of the invention was demonstrated using low-picomoleamounts of phosphotyrosine peptides from the 10-peptide mix and theimmobilized phosphotyrosine antibody P-Tyr-100, as described above inPart IA. P-Tyr-containing phosphopeptides were isolated from thiscomplex mixture, by contacting the 1.0-peptide mix (24 pmol total) withthe P-Tyr-100 antibody-resin (CST product number 9419) (10 μl). Thepeptide mixture contained 100 ng BSA to reduce non-specific peptide lossthrough adsorption. The resin was recovered and washed extensively(twice with 0.5 ml PBS containing 0.5% NP40, twice with 0.5 ml PBS, andfive times with 0.5 ml water). Phosphopeptides bound to theantibody-resin were eluted by washing the resin three times with 5 μl0.1 M glycine, pH 2.3. The three elutions were combined, and an aliquotwas desalted with a ZipTip device (Millipore Corp., part numberZTC18S096), since glycine interferes with MALDI-TOF mass analysis.

FIG. 7 shows the mass spectrum for the low-level 10-peptide mix before(top panel) and after (third panel) immunoaffinity purificationaccording to the method of the invention. Peaks labeled with a starcorrespond to phosphorylated peptides, and peaks labeled with circlescorrespond to the nonphosphorylated partner peptides. All 5phosphopeptides, although present at low (picomole) levels, were boundand eluted from the antibody-resin (third panel). Of the 10 peptides inthe mix, only 3 were detected in the unbound fraction (second panel),and they were all nonphosphorylated peptides. The bound peptide fractionwas neutralized, treated with calf intestinal alkaline phosphatase, anenzyme that can remove phosphate from phosphopeptides, and re-analyzedto confirm the phosphopeptide assignments (FIG. 7, bottom panel). Asexpected, the phosphopeptides were completely dephosphorylated toproduce ions with masses 80 lower than the phosphopeptides. This wasparticularly helpful in assigning the peaks at 1,869 and 1,523 tophosphopeptide synthesis artifacts and the peaks at 1,867 and 1,521 tonon-phosphopeptides. Accordingly, the method of the inventionselectively isolates all desired phosphopeptides, even at low levels,that contain a phosphotyrosine, regardless of the different sequences inwhich the phosphotyrosine occurs, from a low-level mixture ofphosphorylated and nonphosphorylated peptides.

D. Isolation of Akt Substrate Phosphopeptides from a Peptide Mixture

The method of the invention was further demonstrated using amotif-specific, context-independent polyclonal antibody,phospho-(Ser/Thr) Akt substrate antibody, to purify phosphopeptidescontaining the phospho-Akt substrate motif from a mixture ofphosphorylated and nonphosphorylated synthetic peptides. The Akt proteinkinase plays a central role in cell growth (Marte and Downward, TrendsBiochem. Sci. 22: 355-358 (1997)), angiogenesis (Jiang et al., Proc.Natl. Acad. Sci. USA 97: 1749-1753 (2000)), and transcriptionalregulation (Scheid and Woodgett, Curr. Biol. 10: R191-194 (2000)). TheAkt protein kinase is able to phosphorylate protein substrates atthreonine or serine residues when the target residue occurs within theconsensus sequence motif RXRXX(T/S), where R is arginine, X is any aminoacid, and T/S indicates the target threonine or serine.

Phospho-(Ser/Thr) Akt substrate polyclonal antibody (Cell SignalingTechnology, Inc., product number 9611) recognizes a plurality ofdifferent phosphorylated proteins that contain the consensus sequencemotif when phosphorylated, but does not recognize the analogousunphosphorylated motif. The specificity of the phospho-(Ser/Thr) Aktsubstrate antibody is that it binds preferentially to proteins andpeptides that contain phosphothreonine or phosphoserine preceded bylysine or arginine at positions −5 and −3, i.e., (K/R)X(K/R)XX(T*/S*)(SEQ ID NO: 15), in a manner substantially independent of thesurrounding amino acid sequence (i.e. the context of the motif). It isnow demonstrated here that this antibody can be used to purify peptidesthat contain the phosphorylated Akt consensus substrate motif.

Akt motif-containing phosphopeptides were selectively isolated from amixture of phosphorylated and nonphosphorylated synthetic peptidesaccording to the method of the invention. The mixture consisted of 8synthetic peptides: 3 phosphothreonine-containing peptides, 1phosphoserine-containing peptide, and their 4 nonphosphorylated partnerpeptides (Table 3). The phospho-Akt substrate consensus sequence ispresent in all 4 phosphopeptides in this mixture, and it is known fromELISA that these phosphopeptides are recognized by and can bind to thephospho-Akt substrate antibody. TABLE 3 Components of the Phospho-AktSubstrate Peptide Mix Calculated Protonated Sequence Peptide MassCSPRRRAAS*MDNNSKFA 1,989.889 (SEQ ID NO: 16) CSPRRRAASMDNNSKFA 1,909.923(SEQ ID NO: 17) CLKDRQGT*HKDAEIL 1,805.872 (SEQ ID NO: 18)SRPRSCT*WPLPREI 1,777.856 (SEQ ID NO: 19) CRSLT*GKPKLFIIQA 1,754.938(SEQ ID NO: 20) CLKDRQGTHKDAEIL 1,725.906 (SEQ ID NO: 21) SRPRSCTWPLPREI1,696.906 (SEQ ID NO: 22) CRSLTGKPKLFIIQA 1,674.972 (SEQ ID NO: 23)

Phosphopeptides were isolated from this peptide mixture by contactingthe phospho-Akt substrate peptide mix (5 pmol each peptide) withphospho-(Ser/Thr) Akt substrate antibody immobilized to agarose resin(Cell Signaling Technology, Inc., part number 9619) (20 μl, 2 μg/μl).The antibody was incubated with the peptides as a slurry at 4° C. for 2hours. Unbound peptides were removed by centrifugation, and theantibody-resin was washed extensively (two times with 0.5 ml ice-coldPBS containing 0.5% NP-40, two times with 0.5 ml ice-cold PBS, and threetimes with 0.5 ml ice-cold water). Bound peptides were eluted with three101 aliquots of 0.1 M glycine, pH 2.3. A 5 μl portion of the fractioncontaining bound and eluted peptides was desalted and concentrated witha reversed-phase ZipTip microcolumn before analysis by MALDI-TOF massspectrometry, as described above.

FIG. 8 shows the mass spectra of the phospho-Akt substrate peptide mixbefore (top panel) and after (bottom panel) immunoaffinity purification.Peaks labeled with a star correspond to phosphopeptides, peaks labeledwith an open circle correspond to nonphosphorylated peptides, and peakslabeled with a square are phosphopeptides that have undergone metastabledecomposition and neutral-loss of phosphate (discussed in Example Vbelow). The fraction of peptides that bound to and eluted from theimmobilized antibody (bottom panel) contains all 4 phosphopeptides butdoes not contain the nonphosphorylated partner peptides. Accordingly,the method of the invention selectively isolates all peptides in thissynthetic peptide mixture that contain the phospho-Akt substrate motif,whether they contain phosphothreonine or phosphoserine residues. Asdesired, peptides that contain the nonphosphorylated consensus motif arenot isolated.

E. Isolation of 14-3-3 Binding Motif #1 Phosphopeptides from a PeptideMixture

The method of the invention was further exemplified using a secondmotif-specific, context-independent monoclonal antibody, phospho-(Ser)14-3-3 binding motif antibody, to purify phosphopeptides containing the14-3-3 binding motif from a mixture of phosphorylated andnonphosphorylated synthetic peptides. The 14-3-3 proteins regulateseveral biological processes through phosphorylation-dependentprotein-protein interactions (Muslin et al., Cell 84, 889-897 (1996)).Nearly all binding partners of 14-3-3 proteins contain at least one oftwo different phosphoserine-containing consensus sequences (Yaffe et al.Cell 91, 961-971 (1997)). One consensus sequence, motif #1, is(R/K)SXS*XP, where R/K indicates arginine or lysine, S is serine, X isany amino acid, S* is phosphoserine, and P is proline.

Phospho-(Ser) 14-3-3 binding motif monoclonal antibody (4E2) (CellSignaling Technology, Inc., product number 9606) is a motif-specificantibody that recognizes phosphopeptides that contain this consensusbinding motif #1. The 14-3-3 binding motif antibody is highly specificfor peptides and proteins that contain this motif (phosphoserinesurrounded by proline at the +2 position and arginine or lysine at the−3 position, i.e., (K/R)XXS*XP (SEQ ID NO: 24). Recognition is specificfor the phosphorylated form of the motif and is substantiallyindependent of the surrounding amino acid sequence (i.e. the context ofthe motif). This antibody weakly cross-reacts with analogous sequencescontaining phosphothreonine instead of phosphoserine in this motif.

To identify other proteins that bind to 14-3-3 proteins or to profileknown binding partners on a genome-wide (cell-wide) basis, immobilized14-3-3 binding motif antibody may be employed to immunoaffinity purifyphosphopeptides from a proteinaceous preparation in accordance with themethod of the invention. To demonstrate the feasibility of this, thisantibody was first employed to selectively isolate phosphopeptides froma mixture of phosphorylated and nonphosphorylated synthetic peptideswhen the phosphopeptides contain motif sequences that match theantibody's known specificity. The mixture consisted of 13 syntheticpeptides (Table 4). Four peptides in the mixture contained sequencesthat match the antibody's known specificity, 3 with phosphoserine (SEQID NOs: 26, 28, 29) and 1 with phosphothreonine (SEQ ID NO: 27). It isknown by ELISA that these three phosphoserine-containing peptides arerecognized by and can bind to the 14-3-3 binding motif #1 antibody. Thepeptide mixture contained 9 other peptides that should not bind to14-3-3 binding motif antibody: 2 phosphotyrosine-containing peptides, 2phospho-Akt substrate motif peptides, and 5 nonphosphorylated partnerpeptides. TABLE 4 Components of the 14-3-3 Binding Motif Peptide MixCalculated Protonated Sequence Peptide Mass CSPRRRAAS*MDNNSKFA 1,989.889(SEQ ID NO: 25) CSPRRRAASMDNNSKFA 1,909.923 (SEQ ID NO: 26)FRGRSRS*APPNLWAC 1,797.836 (SEQ ID NO: 27) SRPRSCT*WPLPREI 1,777.856(SEQ ID NO: 28) TRSRHSS*YPAGTEEC 1,760.705 (SEQ ID NO: 29)CAEYLRSIS*LPVPVL 1,738.896 (SEQ ID NO: 30) LQERRKY*LKHRC 1,709.878 (SEQID NO: 31) SRPRSCTWPLPREI 1,696.906 (SEQ ID NO: 32) TRSRHSSYPAGTEEC1,680.739 (SEQ ID NO: 33) CAEYLRSISLPVPVL 1,658.929 (SEQ ID NO: 34)MSGRPRTTS*FAESC 1,609.649 (SEQ ID NO: 35) RQGKDY*VGAIPVDC 1,600.719 (SEQID NO: 36) RQGKDYVGAIPVDC 1,520.752 (SEQ ID NO: 37)

A 14-3-3 binding motif #1 antibody (Cell Signaling Technology, Inc.,product number 9606) was linked to agarose resin using a hydrazidechemistry (the same chemistry used to produce the P-Tyr-100 agaroseresin used in Example 1A above), using a commercially availablecrosslinking kit (BiORad Affi-Gel HZ Immunoaffinity Kit, product number153-6060) and following the manufacturer's instructions. Each milliliterof resin was reacted with 1 milligram of antibody. Phosphopeptides wereselectively isolated from the 14-3-3 binding motif peptide mixture bycontacting the peptide mix (10 pmol each peptide) with thisantibody-resin (10 μl, 1 μg/μl). The antibody was incubated with thepeptides as a slurry at room temperature for 1 hour and 4° C. for 1hour. Unbound peptides were removed by centrifugation, and theantibody-resin was washed extensively (twice with 1 ml ice-cold PBS andonce with 1 ml ice-cold water). Bound peptides were eluted with one 30μl aliquot of 0.1 M glycine, pH 2.0. A 9 μl portion of the elutedpeptides was desalted and concentrated with a reversed-phase ZipTipmicrocolumn before analysis by MALDI-TOF mass spectrometry, as describedabove.

The mass spectra of the peptide mix before (top panel) and after (bottompanel) immunoaffinity purification are shown in FIG. 9. Peaks labeledwith a star correspond to phosphopeptides, and peaks labeled with anopen circle correspond to nonphosphorylated peptides. Peaks labeled withfilled stars are phosphopeptides that are not expected to bind to the14-3-3 binding motif antibody because their sequences do not fit theantibody's known specificity. Of the four phosphopeptides in the mixturethat contain the 14-3-3 binding motif, three were isolated by the 14-3-3binding motif antibody, and they correspond to the major peaks in thefraction of peptides that bound to and eluted from the immobilizedantibody (FIG. 9, bottom panel). One 14-3-3 binding motif phosphopeptidewas not isolated (SEQ ID NO: 29, calculated protonated peptide mass of1,738.9), but it also could not be detected in the untreated peptidemix, i.e. it may be a poorly ionizing peptide. Thephosphothreonine-containing peptide, which contains a slightly variantmotif (phosphothreonine in place of phosphoserine), was also isolated(SEQ ID NO: 27, calculated protonated peptide mass of 1,777.8); it was,in fact, expected to cross-react weakly with the antibody. Two peptidesthat do not contain sequences that match the antibody's specificity wereisolated, one was a phosphopeptide containing the phospho-Akt substratemotif (SEQ ID NO: 35, calculated protonated peptide mass of 1,608.6) andthe other was unphosphorylated (SEQ ID NO: 25, calculated protonatedpeptide mass of 1,910.9). Several peaks in the bound and eluted fraction(1,941, 1,770, 1,642, 1,526) are also present in the bound and elutedfraction of a negative control, antibody-resin treated with bufferinstead of peptide mixtures. These artifactual peaks appear to originatefrom the antibody-resin preparation and can probably be avoided bymanufacturing a new lot of antibody-resin from highly purified antibodyor by pre-eluting the antibody-resin before applying peptide mixtures.

This result further establishes the generality of the method of theinvention by showing that desired phosphopeptides can beisolated/enriched by immunoaffinity purification, as described herein.As previously discussed, in certain cases, as here, some peptides thatcontain the target sequence motif may not be isolated, and/or otherpeptides that do not contain the target motif may be inadvertently orartifactually purified, for reasons that are unclear. Nevertheless, thecompleteness and specificity of the disclosed method represents asubstantial advance over alternative phosphopeptide purificationmethods. As previously described, it is anticipated that, in cases whereundesired peptides lacking the target motif are co-isolated along withdesired peptides, the former may be avoided by increasing the number orstringency of the resin washes to remove non-specifically boundpeptides.

EXAMPLE II

A. Isolation of Phosphotyrosine-Containing and Phospho-Akt SubstratePeptide Subsets from a Digested Crude Cell Extract

Example I demonstrates that several phosphorylation-specific antibodiescan be employed in the method of the invention to selectively separatedesired phosphopeptides from non-phosphopeptides. The antibodies may begeneral modification-specific antibodies or motif-specific,context-independent antibodies that recognize a short non-unique motifcomprising several invariant residues, which motif is present on aplurality of different peptides or proteins within a genome. As shown inExample I, the antibodies can distinguish phosphopeptides fromnon-phosphopeptides even when the only difference between the peptidesis the presence or absence of a phosphate group. In the present Example,it is shown that desired phosphopeptides may be selectively isolated bythe method of the invention from a complex mixture containingphosphopeptides of different types. The method of the invention isolatesthe phosphopeptide subset that would be expected on the basis of theantibody's specificity. It is also shown that the results obtained byapplying the method to crude cell extracts closely resemble the resultsobtained by applying the method to well-defined synthetic peptidemixtures.

The exemplary preparation for the isolation described herein wascomposed of a digested crude cell extract to which the phosphotyrosinepeptide mix and the phospho-Akt substrate peptide mix have been added.The crude cell extract was made from 3T3 mouse fibroblast cells that hadbeen stably transfected to express active Akt protein kinaseconstituitively and that had been treated with 50 ng/ml platelet-derivedgrowth factor (PDGF) for 15 minutes. The cells were washed, harvested,and lysed by sonication, proteins in the lysate were denatured, and thelysate was cleared by centrifugation. The extract was then digested topeptides with endoproteinase Glu-C immobilized to F7m, a polyvinylmatrix bead (MoBiTec, part number P5101), and the immobilized Glu-C wasremoved by centrifugation. The digested extract was treated withphospho-(Ser/Thr) Akt consensus substrate motif antibody (Cell SignalingTechnology, Inc., product number 9611) to remove endogenous peptidesrecognized by this antibody.

This depleted digested extract was mixed with the phosphotyrosinepeptide mix (Table 1) and the phospho-Akt substrate peptide mix (Table3), so that each peptide was present at a concentration of 10 pmol/mland the background of peptides from the digested extract was 250 μg/ml.This peptide-extract mixture (1 ml) was treated with either immobilizedP-Tyr-100 antibody (Cell Signaling Technology, Inc., part number 9419)or immobilized phospho-Akt substrate antibody (20 μl, 2 μg/μl). After 2hours at 4° C., each antibody-resin was collected by centrifugation andextensively washed (three times with 1 ml ice-cold PBS and two timeswith 1 ml ice-cold water). Bound peptides were then eluted with two 15μl aliquots of 0.1 M glycine, pH 2.3. Before analysis by MALDI-TOF massspectrometry, as described above, a 9 μl portion of the fractioncontaining bound and eluted peptides was desalted and concentrated witha reversed-phase ZipTip microcolumn.

For P-Tyr-100 antibody, a general modification-specific antibody, thespectrum shows that the antibody isolated 3 of the 5 phosphotyrosinepeptides but none of the 4 phospho-Akt substrate phosphopeptides, whichdo not contain phosphotyrosine, and none of the 9 non-phosphopeptides,as expected due to the antibody's specificity (FIG. 10, top panel).Peaks labeled with a star correspond to phosphopeptides, and peakslabeled with an open circle correspond to nonphosphorylated peptides.Comparison to FIG. 4 shows the 2 phosphotyrosine-containing peptidesthat were not identified from the peptide-extract mixture gave lowsignals from a relatively simple mixture of synthetic peptides. Thesepeptides may ionize poorly when other peptides are present because theypoorly compete for protons.

For the phospho-Akt substrate antibody, a motif-specific,context-independent antibody, the spectrum shows the antibody isolated 3of the 4 phosphopeptides from the phospho-Akt substrate peptide mix butnone of the 5 phosphotyrosine peptides (FIG. 11, top panel). Comparisonto FIG. 8 shows that the single phospho-Akt substrate peptide that wasnot identified from the peptide-extract mixture gave low signals from asynthetic peptide mix.

The phosphopeptide assignments shown in FIGS. 10 and 11 were confirmedby treating a portion of the bound peptide fraction with calf-intestinalphosphatase, which can remove phosphate from phosphopeptides. Asexpected, most assigned phosphopeptides were dephosphorylated to produceions with masses 80 lower than the phosphopeptides (FIGS. 10 and 11,bottom panels). Accordingly, desired phosphopeptides may be selectivelyisolated from a complex mixture according to the method of theinvention.

B. Isolation of Phosphopeptides Containing the 14-3-3 Binding Motif froma Digested Crude Cell Extract

As another example confirming that results obtained with crude cellextracts closely resemble the results obtained with well-definedsynthetic peptide mixtures, the method of the invention was employed toisolate 14-3-3 binding motif-containing phosphopeptides from a complexmixture comprising a cell extract and a mixture of synthetic peptides.

The exemplary preparation for the isolation described herein wascomposed of a digested crude cell extract to which the 14-3-3 bindingmotif #1 peptide mix (Table 4) has been added. An endoproteinaseGlu-C-digested crude cell extract was prepared from 3T3 mouse fibroblastcells stably transfected to express active Akt protein kinaseconstitutively, as described in Example II(A) above. This digestedextract was mixed with the 14-3-3 binding motif peptide mix (Table 4),so that each peptide was present at a concentration of 10 pmol/ml andthe background of peptides from the digested extract was 0.5 mg/ml.

Immobilized 14-3-3 binding motif antibody was prepared by mixing 1 mg of14-3-3 binding motif antibody and 0.1 ml of protein Aagarose resin(Roche, product number 1 134 515) overnight at 4° C. Unbound antibodywas removed by washing the resin three times with cold PBS. The amountof antibody bound to protein Aagarose was shown to be

4 mg antibody/ml resin by measuring the absorbance at 280 nm of theantibody solution before and after immobilization.

The peptide-extract mixture (1 ml) was treated with immobilized 14-3-3binding motif #1 antibody (20 μl, 1 μg/μl). After 2 hours at 4° C., theantibody resin was collected by centrifugation and extensively washed(twice with 1 ml ice-cold PBS and once with 1 ml ice-cold water). Boundpeptides were then eluted with one 30 μl aliquot of 0.1% trifluoroaceticacid. Before analysis by MALDI-TOF mass spectrometry, as describedabove, a 9 μl portion of the fraction containing bound and elutedpeptides was desalted and concentrated with a reversed-phase ZipTipmicrocolumn.

FIG. 12 shows the peptides that were bound and eluted from the 14-3-3antibody-resin. Peaks labeled with a star correspond to phosphopeptides,and peaks labeled with an open circle correspond to nonphosphorylatedpeptides. Comparison of FIG. 12 and FIG. 9 shows the method isolated thesame four 14-3-3 motif phosphopeptides from the synthetic peptide mix,even when the mixture was diluted into a large background of potentiallyinterfering, non-binding peptides from a digested cell extract.Accordingly, desired phosphopeptides may be selectively isolated from acomplex mixture according to the method of the invention.

EXAMPLE III Isolation of Phosphotyrosine-Containing Peptides from AnExtract of Cells Overexpressing Epidermal Growth Factor Receptor

The selective isolation of modified peptides from a complex mixtureaccording to the method of the invention was further demonstrated usinga digested whole cell extract and a general phosphotyrosine antibody toisolate known phosphopeptides. A model system, the A431 epidermoidcarcinoma cell line overexpressing the human epidermal growth factorreceptor (EGFR), was selected since the modification (phosphorylation)of sites on this protein is well-studied. Activation of EGFR familymembers is associated with many tumors. Five sites of in vivoautophosphorylation have been identified in EGFR: three major sites(Tyr-1068, Tyr-1148, and Tyr-1173) and two minor sites (Tyr-992 andTyr-1086) (Downward et al., J. Biol. Chem. 260:14538-546 (1985); Hsuanet al., Biochem. J. 259: 519-27 (1989); Margolis et al., EMBO J. 9:4375-380 (1990); Walton et al., J. Biol. Chem. 265:1750-54 (1990)). EGFRis the major phosphorylated protein expected to be expressed in thiscell line.

A cell preparation was obtained as follows: A431 cells were treated with20 ng/ml EGF for 5 minutes and then washed and harvested. The cells werelysed by sonication, proteins in the lysate were denatured, and thelysate was cleared by centrifugation. The cell extract was analyzed bySDS-PAGE and Western blotting to show the level of phosphorylated EGFR(FIG. 13). Compared to untreated cells (FIG. 13, lane 1), the majorprotein recognized by P-Tyr-100 antibody in EGF-treated cells is EGFR(lane 2). Proteins in the extract supernatant were digested to peptideswith trypsin immobilized to POROS resin (Applied Biosystems, part number2-3127-00), and the immobilized trypsin was removed by centrifugation.

To selectively isolate phosphotyrosine-containing peptides from thecomplex mixture of peptides contained in the proteinaceous preparation,the trypsin-digested crude extract (about 2.5 mg protein/mL) wascontacted with an immobilized general tyrosine modification antibody,P-Tyr-100 antibody-resin (Cell Signaling Technology, Inc., productnumber 9419) (20 μl). The slurry was incubated and processed asdescribed above, except that the first wash was with 0.5 ml PBScontaining 0.1% Tween 20. FIG. 14 (top panel) shows the mass spectrumfor the bound peptide fraction from this complex mixture (digest). Peakslabeled with a star correspond to two known phosphotyrosine sites in EGFreceptor: the protonated tryptic peptide containing pTyr-1148 has anexpected mass of 2,316.0, and the peptide containing pTyr-1086 has anexpected mass of 2,479.2. Note that these EGF receptor peptides wereexpected to be the major phosphotyrosine peptides in the bound fraction,because the cell line overexpresses the EGF receptor.

To confirm these assignments, the isolated (i.e. bound) peptide fractionwas treated with a phosphatase enzyme, as described above, and thetreated fraction re-analyzed by MALDI-TOF mass spectrometry, asdescribed above (FIG. 14, bottom panel). As expected, these twophosphopeptides were completely dephosphorylated to produce new ionswith masses 80 lower than the phosphopeptides, corresponding to theremoval of one phosphate group from each peptide. Accordingly, themethod of the invention selectively isolates modified peptides, e.g.those containing phosphotyrosine, from a complex mixture that is presentin a proteinaceous preparation (digested crude cell extract). Similarisolations may be carried out for any desired proteinaceous preparationusing a desired, immobilized modification-specific antibody.

EXAMPLE IV Isolation of Phosphotyrosine-Containing Peptides from anExtract of Cells Expressing Activated Src Protein Kinase or ActivatedAbl Protein Kinase

To demonstrate that the set of phosphopeptides isolated by the generalphosphotyrosine antibody is a property of the cell extract, the methodof the invention was applied to a digested whole cell extract differentfrom the one used in Example III. Here, the exemplary system is 3T3mouse fibroblast cells stably transfected to express active Src proteinkinase constituitively. The Src family of protein kinases is importantin the regulation of cell growth and differentiation (Thomas and Brugge,Annu. Rev. Cell. Dev. Biol. 13, 513-609 (1997)). Src protein kinaseparticipates in many different signaling pathways and can affect diversebiological processes. Src is known to phosphorylate its target proteinson Tyr residues, i.e., it is a tyrosine-specific kinase.

A digested cell extract was prepared by harvesting 3T3 cells expressingSrc protein kinase. The cells were lysed by sonication, proteins in thelysate were denatured, and the lysate was cleared by centrifugation. Toshow that activated Src protein kinase had phosphorylated many targetproteins, the cell extract was analyzed by SDS-PAGE and Western blotting(FIG. 15). Activation of Src protein kinase was shown by blottingextracts of untransfected (lane 1) and Src-transfected (lane 2) 3T3cells and probing the blot with P-Tyr-100 antibody (Cell SignalingTechnology, Inc., product number 9411). The level and extent of tyrosinephosphorylation was much greater in cells that had been stablytransfected with Src protein kinase than in untransfected cells.

Proteins in the extract were digested to peptides with immobilizedtrypsin, and the immobilized trypsin was removed by centrifugation.Immobilized P-Tyr-100 antibody was prepared by mixing 1 mg of P-Tyr-100and 0.1 ml of protein G-agarose resin (Roche, product number 1 243 233)overnight at 4° C. Unbound antibody was removed by washing the resinthree times with cold PBS. The amount of antibody bound to proteinG-agarose was shown to be 5 mg antibody/ml resin by measuring theabsorbance at 280 nm of the antibody solution before and afterimmobilization.

Phosphotyrosine-containing peptides were isolated from the complexmixture of peptides contained in the proteinaceous preparation bycontacting the trypsin-digested extract (about 12 mg, 1 mg/ml) withphosphotyrosine antibody P-Tyr-100 that was bound to protein G resin (20μl, 5 mg antibody/ml resin) in batch format at 4° C. for 16 hours.Unbound peptides were removed by centrifugation, and the antibody-resinwas extensively washed (three times with 1 ml ice-cold PBS and twicewith 1 ml ice-cold water). Bound peptides and antibody were then elutedwith 100 μl of 0.1% trifluoroacetic acid, and the eluted peptides wereseparated from eluted antibody by centrifugation through a MicroconYM-10 membrane (Millipore, product number 42407), which retainsmolecules with molecular weights above 10,000. Before analysis byMALDI-TOF mass spectrometry, a 9 μl portion of the YM-10 flow-throughfraction was desalted and concentrated with a reversed-phase ZipTipmicrocolumn.

The masses of the peptides that bound to and eluted from thephosphotyrosine antibody were measured by MALDI-TOF mass spectrometrybefore (FIG. 16, top panel) and after (bottom panel) treating thepeptide fraction with shrimp alkaline phosphatase, which can removephosphate groups from phosphopeptides and produce ions with masses 80lower than phosphopeptides for each phosphate group in the peptide, toconfirm the eluted peptides are phosphorylated (FIG. 16, bottom panel).The masses of eight peptides bound and eluted from phosphotyrosineantibody-resin gave new ions with masses 80 lower than thephosphopeptides after treatment with phosphatase, indicating they arephosphopeptides.

The peptides that bound to and eluted from the phosphotyrosine antibodywere further analyzed by LC-MS/MS. A 25 μl portion of the peptidefraction was desalted and concentrated with a reversed-phase ZipTipmicrocolumn and eluted with 2 μl 0.1% trifluoroacetic acid, 40%acetonitrile. An 0.4 μl aliquot of the eluted fraction was mixed with anACHA matrix solution and analyzed by MALDI-TOF mass spectrometry, and itgave a spectrum similar to the one shown in FIG. 16. The remainder ofthe eluted fraction was analyzed by LC-MS/MS.

LC-MS/MS analysis was performed with a ThermoFinnigan Surveyor HPLCsystem coupled to a ThermoFinnigan LCQ Deca ion trap mass spectrometer.To reduce its acetonitrile concentration to a level that would allowpeptides to bind to a reversed-phase support, the sample was diluted10-fold with 0.5% acetic acid, 0.005% HFBA (heptafluorobutyric acid,Pierce Endogen, part number 25003), 5% acetonitrile containing 1% formicacid. Using a pressure cell, the diluted sample was loaded onto acapillary column (75 μm internal diameter, 15 μm tip, fused silicaPicoTip, New Objective, part number FS360-75-15-N) that had been packedwith Magic C18AQ reversed-phase resin (5 μm particles, 100 Angstrompores, Michrom Bioresources, part number 9996610000) and equilibratedwith 0.5% acetic acid, 0.005% HFBA, 5% acetonitrile. Peptides wereeluted from the column by a linear gradient of increasing acetonitrileconcentration at a nominal flow rate of 250 nl/min.

To induce electrospray at the tip of the column, 2,000 V was applied toa liquid junction upstream of the column at a cross used to modulate theflow rate from the HPLC pump, as described by Gatlin et al., supra.ThermoFinnigan Xcalibur software was used for instrument control anddata acquisition. As peptides eluted from the LC column, MS/MS spectrawere collected in a “top-three” data-dependent manner: the methodperformed a survey MS scan and then collected MS/MS spectra for thethree most abundant ions, if they were above a pre-set intensitythreshold and if they were not recently analyzed by MS/MS already(recognized by using the dynamic exclusion feature of Xcalibursoftware).

Peptides were identified by analyzing all the MS/MS product ion spectrawith Sequest, a program that correlates an experimental spectrum to alibrary of theoretical spectra derived from protein sequence databasesto find a best-fit match. One unambiguously identified phosphopeptide isa phosphotyrosine-containing peptide from enolase A (FIG. 17), anabundant enzyme. The residue identified as a phosphorylation site bythis method is known to be phosphorylated in cells transfected with Src(see, e.g. Tanaka et al. J. Biochem (Tokyo) 117: 554-559 (1995) andCooper et al. J. Biol. Chem. 259: 7835-7841 (1984)). This phosphopeptidecorresponds to a prominent peak detected during MALDI-TOF massspectrometry, labeled “1,885.2” in FIG. 16, demonstrating, the samephosphopeptides detected during MALDI-MS can be further analyzed byLC-MS.

Accordingly, immunoaffinity isolation of modified peptides by thedisclosed method detected a site known to be phosphorylated under thesecell culture conditions and, as expected, the assigned site fits theantibody's known specificity. This result, isolation of a known enolasephosphopeptide from a digested extract of mouse cells, is in starkcontrast to the results reported in Marcus et. al., supra., where,following the failure to isolate a phosphotyrosine-containing peptidefrom gel-purified human enolase (the same protein), it was expresslyconcluded that immunoaffinity purification of phosphopeptides is almostimpossible.

In a separate study the method of the invention was used to extractphosphotyrosine peptides from NIH/3T3 cells expressing one of twoconstituitively active tyrosine kinases, v-Abl and c-Src Y527F. Thesecell lines were left untreated during cell culturing so the bulk of thetyrosine phosphorylation in the cell is expected to originate from theaction of the constituitively active kinase expressed in the cell. Theobjective was to determine whether the method of the invention can beused to detect phosphorylation indicative of Abl or Src activation inthe same cellular background.

Lysates were prepared from 2×10⁸ cells for both cell lines and digestedin 2 M urea with trypsin after treatment with DTT and iodoacetamide toalkylate cysteine residues. Before the immunoaffinity step, peptideswere prefractionated by reversed-phase solid phase extraction usingSep-Pak C₁₈ columns (1 ml column volume per 2×10⁸ cells) to separatepeptides from other cellular components. The solid phase extractioncartridges were eluted with steps of 5, 15, 25, and 40% acetonitrile.Each lyophilized peptide fraction was redissolved in 1 ml PBS andtreated with phosphotyrosine antibody (P-Tyr-100, Cell SignalingTechnology product number 9411) immobilized on protein G-Sepharose(Roche) (60 μg antibody, 15 μl resin) overnight at 4° C. Antibody-resinwas thoroughly washed, and immunoaffinity-purified peptides were elutedwith 75 μl of 0.1% TFA. A portion of this fraction (40 μl) wasconcentrated with Stage tips and analyzed by LC-MS/MS, using aThermoFinnigan LCQ Deca XP Plus ion trap mass spectrometer. Peptideswere eluted from a 10 cm×75 μm reversed-phase column with a 45-minlinear gradient of acetonitrile delivered at 280 nl/min. MS/MS spectrawere evaluated using the program Sequest with the NCBI mouse proteindatabase.

More phosphopeptides were found in 3T3-Src (179) than in 3T3-Abl (83),which was consistent with the level of phosphotyrosine detected bywestern blotting. Substantial overlap was observed between the tyrosinephosphorylation sites found in 3T3-Abl and in 3T3-Src: 62 of the 186phosphotyrosine sites found in 3T3/Src were also found in 3T3-Abl. Theoverlap may be attributed to activation of a Src-like kinase in 3T3-Ablcells, which were found to contain IIEDNEpYTAR, the activation loopphosphopeptide from the Src-family members Hck and Lyn, or LIEDNEpYTAR,which is found in other Src-family members such as Fyn, Lck, Src, andYes. It is clear that at least one Src-family kinase has been activatedin 3T3-Abl cells, but we cannot specify the activated enzyme becauseSrc-family kinases are so closely related and these two peptides haveidentical mass. Some of the phosphotyrosine sites from known cellsignaling proteins found in 3T3-Abl and 3T3-Src are shown in Table 5.TABLE 5 Selected phosphopeptides found in 3T3-Abl and 3T3-Src ProteinName‡ Abl Src Sequence Tyrosine kinase * Eph receptor •VLEDDPEATpYTTSGGK   A2 * Eph receptor • • VLEDDPEAApYTTR   A4   Ephreceptor • VYIDPFTpYEDPNEAVR   B3   focal adhesion • •THAVSVSETDDpYAEIIDEEDTYTMPS   kinase TR * focal adhesion • • YMEDSTpYpYK  kinase   focal adhesion • GSIDREDGSFQGPTGNQHIpYQPVGKP   kinaseDPAAPPK * hemopoietic • • IIEDNEpYTAR   cell kinase * fer protein •QEDGGVpYSSSGLK   kinase * Src • LIEDNEpYTAR Ser/Thr kinase   cdc2a • •IGEGTpYGVVYK * DYRK1a • • IYQpYIQSR   DYRK3 • pYEVLKIIGKGSFGQVAR * GSK3beta • • GEPNVSpYICSR * HIPK 1 • • AVCSTpYLQSR * HIPK 3 • TVCSTpYLQSR *MAPK1 • VADPDHDHTGFLTEpYVATR * p38 MAP Kinase • HTDDEMTGpYVATR  pre-mRNA • • LCDFGSASHVADNDITPpYLVSR   protein kinase   Cdc42 BP •LPDFQDSIFEpYFNTAPLAHDLTFR   kinase beta Adaptor   abl-interactor •TLEPVKPPTVPNDpYMTSPAR   1   caveolin • • YVDSEGHLpYTVPIR   Cbl-b • •ASQDpYDQLPSSSDGSQAPARPPKPR   DOK1 • • TVPPPVPQDPLGSPPALpYAEPLD SLR  DOK1 • • IPPGPSQDSVpYSDPLGSTPAGAGEGV HSK   DOK1 • •LTDSKEDPIpYDEPEGLAPAPPR   DOK1 • LKEEGYELPYNPATDDpYAVPPPR   DOK1 • •GFSSDTALpYSQVQK   GAB1 • DASSQDCpYDIPR   p130 Cas • •TQQGLpYQAPGPNPQFQSPPAK   p130 Cas • VGQGYVYEAAQTEQDEpYDTPR   p130 Cas •• EETpYDVPPAFAK   PI3K p85 beta • • EYDQLpYEEYTR   subunit   SHB adaptor• VTIADDpYSDPFDAK   protein   Shc1 • • ELFDDPSpYVNIQNLDK   similar toSHB • • LDpYCGGGGGGDPGGGQR   adapt. pro. B   Crk • RVPCApYDK   disabled• GPLNGDTDpYFGQQFDQLSNR   homolog 2   DOK1 • KPLpYWDLpYGHVQQQLLK   DOK1• GLpYDLPQEPR   DOK1 • LKEEGpYELPpYNPATDDpYAVPPPR   HGF reg. tyr. •VCEPCpYEQLNK   kinase subs.   intersectin 2 • GEPEALpYAAVTK   p130 Cas •VGQGYVpYEAAQTEQDEpYDTPR   p130 Cas • HPLILAAPPPDSPAAEDVpYDVPPPAPDLpYDVPPGLR   p130 Cas • VLPPEVADGSVVDDGVpYAVPPPAER   PI3K p85 reg. •LNEWLGNENTEDQpYSLVEDDEDLPH   subunit HDEK   PLC gamma 1 •IGTAEPDpYGALYEGR   Shc1 • MAGFDGSAWDEEEEEPPDHQpYpYNDF PGK   Src-assoc. •SVYLQEFQDKGDAEDGDEpYDDPFAGP   adaptor ADTISLASER   protein   Src-assoc.• IpYQFTAASPK   adaptor   protein   Src-assoc. •SQPIDDEIpYEELPEEEEDTASVK   adaptor   protein   Stam2 • LVNEAPVYSVpYSK  Wiskott- • VIpYDFIEK   Aldrich syn.-   like‡ * indicates activation loop peptides.• indicates phosphopeptides found in 3T3-Abl or 3T3-Src.

In 3T3-Src cells, phosphorylation was detected in the activation loop ofa Src-family kinase, most likely Tyr-424 of Src. Tyrosinephosphorylation was also found in proteins that are known to besubstrates of Src, e.g., the non-receptor tyrosine kinase FAK, theadaptor protein p130Cas, the actin-binding protein cortactin, thephospholipid-binding protein annexin A2, and the STAM-interactingprotein Hrs. FAK was phosphorylated at Tyr-397, which creates a bindingsite for Src-family kinases, and at its activation loop sites Tyr-576and Tyr-577, which are known to be phosphorylated by Src-family kinases.Seven tyrosine phosphorylation sites were found in p130Cas, all in theSrc-substrate region of p130Cas and six containing the YXXP motif, whichwhen phosphorylated results in the interaction of p130Cas with severalsignaling proteins. Some phosphorylation sites map to putative Srcsubstrates, e.g., SCAP2 is a homolog of the Src-associatedphosphoprotein SKAPP55 and was found to be phosphorylated at Tyr-260,which in SKAPP55 is thought to be phosphorylated by the Src-familykinase Fyn.

EXAMPLE V Isolation of Peptides Containing the Phospho-(Ser) PKCSubstrate Motif from an Extract of Jurkat Cells Treated withTetradecanoyl Phorbol Acetate

The method of the invention was further demonstrated using amotif-specific, context-independent polyclonal antibody, phospho-(Ser)PKC substrate motif antibody, to purify phosphopeptides containing thephospho-(Ser) PKC substrate motif from a digested whole cell extract.Protein kinase C (PKC) family members are involved in a number ofcellular processes such as secretion, gene expression, proliferation andmuscle contraction (see e.g. Nishikawa et al. J. Biol. Chem. 272:952-960 (1997) and Pearson and Kemp Methods Enzymol. 200: 62-81 (1991)).Conventional PKC isozymes phosphorylate protein substrates at serine orthreonine residues when the target residue occurs within the consensussequence motif (R/K)(R/K)X(S/T)(hyb)(R/K) (SEQ ID NO: 38), where R/Kindicates arginine or lysine, X is any amino acid, S/T indicates thetarget serine or threonine, and hyb is a hydrophobic amino acid.

Phospho-(Ser) PKC substrate motif antibody (Cell Signaling Technology,Inc., product number 2261) recognizes a plurality of differentphosphorylated proteins that contain the consensus sequence motif whenphosphorylated but does not recognize the analogous unphosphorylatedmotif. The specificity of the phospho-(Ser) PKC substrate antibody isthat it binds preferentially to proteins and peptides that containphosphoserine preceded by arginine or lysine at positions −2 and +2 anda hydrophobic residue at the +1 position, i.e., (R/K)XS*(hyb)(R/K) (SEQID NO: 39), in a manner substantially independent of the surroundingamino acid sequence. The antibody does not recognize thenon-phosphorylated motif or the motif containing phosphothreonine. It isdemonstrated here that this antibody can be used in accordance with themethod of the invention to purify peptides that contain thisphospho-(Ser) PKC substrate motif, to identify other proteins that maybe phosphorylated by conventional PKC isozymes on a genome-wide(cell-wide) basis.

For this example, the model system was Jurkat cells, a human cell linederived from an acute T cell leukemia, that had been treated for 10minutes with a potent activator of protein kinase C, tetradecanoylphorbol acetate (TPA). The cells were washed, harvested, and lysed bysonication, proteins in the lysate were denatured, and the lysate wascleared by centrifugation.

To show that TPA had activated protein kinase C and caused an increasedlevel of PKC-specific protein phosphorylation, the cell extract wasanalyzed by SDS-PAGE and Western blotting (FIG. 18). Induction of PKCsubstrate phosphorylation was shown by probing a blot of TPA-treatedcell extract (lane 2) and untreated cell extract (lane 1) withphospho-(Ser) PKC substrate antibody (Cell Signaling Technology, Inc.,product number 2261). This showed that TPA treatment altered thephosphorylation state of a large number of different proteins thatcontain the phospho-(Ser) PKC substrate motif.

Proteins in the extract were digested to peptides with endoproteinaseGlu-C immobilized to F7m, a polyvinyl matrix bead (MoBiTec, part numberP5101), and the immobilized Glu-C was removed by centrifugation.Immobilized phospho-(Ser) PKC substrate antibody was prepared asdescribed above for immobilized P-Tyr-100 antibody (Example IV). Theimmobilized antibody was evaluated as described above and found tocontain 4 mg antibody per ml of resin.

Phosphopeptides containing the phospho-(Ser) PKC substrate motif werepurified from the Glu-C-digested crude cell extract with the antibodyimmobilized to protein G-agarose resin. The digest (about 40 mg, 1 mg/mlprotein) was contacted with immobilized antibody-resin (40 μl, 4 mg/ml)in batch format at 4° C. for 16 hours, and unbound peptides were removedby centrifugation. The antibody-resin was washed extensively (threetimes with 1 ml ice-cold PBS and twice with 1 ml ice-cold water). Boundpeptides were then eluted with 150 μl 0.1% trifluoroacetic acid, and theeluted peptides were separated from eluted antibody by centrifugationthrough a Microcon YM-10 membrane (Millipore, product number 42407),which retains molecules with molecular weights above 10,000. Beforeanalysis by MALDI-TOF mass spectrometry, a 9 μl portion of the YM-10flow-through fraction was desalted and concentrated with areversed-phase ZipTip microcolumn.

MALDI-TOF Analysis

The masses of the peptides that bound to and eluted from thephospho-(Ser) PKC substrate antibody were measured by MALDI-TOF massspectrometry (FIG. 19, top panel). Phosphatase treatment and metastabledecomposition (bottom panel) showed that the antibody-purified peptidefraction contains several candidate phosphopeptides with phosphoserineor phosphothreonine, as expected based on the antibody's specificity. InFIG. 19, peaks labeled with a star correspond to phosphopeptides, peakslabeled with an open circle correspond to nonphosphorylated peptides,and peaks labeled with a square are phosphopeptides that have undergonemetastable decomposition and neutral-loss of phosphate.

Phosphopeptide peaks detected during MALDI-TOF mass spectrometry (FIG.19, top panel) are accompanied by companion peaks that are broader andapparently 84 lower in mass, e.g., the peak with a mass of 1989 has apartner peak at 1905, etc. These companion peaks correspond tometastable decomposition products of phosphopeptides, formed byneutral-loss of phosphate while the phosphopeptide ions are traveling tothe detector of the mass spectrometer. The peaks for decompositionproducts are broader than the peaks for phosphopeptides because thedecomposition products form after ionization and the instrument isconfigured to focus ions that are stable during analysis. For similarreasons, the expected mass shift for loss of phosphate is −98, but −84mass shifts are observed because, unlike a stable ion, the mass of adecomposition product changes during analysis. Metastable decompositionof phosphopeptides has been noted by others and can be used to recognizeand assign phosphopeptides in a MALDI-TOF mass spectrum (Annan and Carr,supra.). Analysis of a large number of synthetic phosphopeptides byMALDI-TOF mass spectrometry indicates that some peptides containingphosphoserine or phosphothreonine (but not phosphotyrosine) residuesundergo metastable decomposition. For this reason, metastabledecomposition is a reliable indicator of peptides that containphosphoserine or phosphothreonine.

The phosphorylation state of the peptide fraction was also evaluated bytreating it with shrimp alkaline phosphatase, which can remove phosphategroups from phosphopeptides to produce ions with masses 80 lower thanphosphopeptides for each phosphate group in the peptide. Allphosphopeptide candidates were affected by phosphatase treatment, andfour phosphopeptides gave dephosphorylated peptides that were 80 lowerin mass than the peptides before treatment (FIG. 19, bottom panel).

LC-MS/MS Analysis

The peptides that bound to and eluted from the phospho-(Ser) PKCsubstrate motif antibody were further analyzed by LC-MS/MS. A 40 μlportion of the peptide fraction was desalted and concentrated with areversed-phase ZipTip microcolumn and eluted with 2 μl 0.1%trifluoroacetic acid, 40% acetonitrile. An 0.4 μl aliquot of the elutedfraction was mixed with an ACHA matrix solution and analyzed byMALDI-TOF mass spectrometry, and it gave a spectrum similar to the oneshown in FIG. 19. An 0.8 μl aliquot of the eluted fraction was analyzedby LC-MS/MS.

LC-MS/MS analysis was performed as described above (Example IV). Thechromatogram obtained by analyzing this sample is shown in FIG. 20. Thefirst panel of FIG. 20 shows where survey MS scans were collected, andthe second panel shows where MS/MS spectra were collected. The third,fourth, and fifth panels show where neutral loss of 49, 32.7, and 24.5,respectively, was detected. During the fragmentation process of MS/MS,peptides containing phosphoserine or phosphothreonine often form an ionby simple loss of phosphate to produce a neutral-loss ion that has amass 98 lower than the unfragmented parent ion. If the parent ion has acharge of +1, the neutral-loss ion has a mass-to-charge value (m/z) of98/1 or 98 lower than the parent ion mass-to charge value. Likewise,phosphopeptide parent ions with charges of +2, +3, or +4 will giveneutral-loss ions with m/z values that are 49, 32.7, and 24.5 lower thanthe parent ion. The occurrence and intensities of neutral-loss ions areplotted in the third, fourth, and fifth panels of FIG. 20 to help locatecandidate phosphopeptides. The neutral loss plots show thatphosphopeptide candidates tend to elute early in the chromatogram, asexpected for phosphopeptides due to the hydrophilicity of phosphategroups, and that neutral loss is observed in many of the MS/MS spectra,suggesting this sample is highly enriched with phosphopeptides.

As discussed, neutral loss during MS/MS is the same process asmetastable decomposition during MALDI-TOF mass spectrometry. Asexpected, many of the phosphopeptides showing neutral loss duringLC-MS/MS (FIG. 20, panels 3-5) are the same phosphopeptides that gavemetastable decomposition during MALDI-TOF mass spectrometry (FIG. 19,top panel), see FIG. 21. For each neutral-loss MS/MS spectrum, theparent ion mass (m) can be calculated from the parent ion mass-to-chargevalue (m/z) and the charge (z) inferred from the neutral loss value (+2for neutral loss of 49, +3 for 32.7, and +4 for 24.5). Some individualpeptides were observed to undergo neutral loss as +2, +3, and +4 ions.For example, LC-MS/MS spectra 533, 534, and 535 show neutral loss andcorrespond to +4, +3, and +2 ions, respectively, of a candidatephosphopeptide labeled “2,413.3” in FIG. 19. Both MALDI-TOF massspectrometry and LC-MS/MS give this peptide a mass of 2,413, and theneutral loss observed during both mass analysis methods show the peptidecontains one phosphate. A comparison of datasets shows the same peptidesare detected by both mass analysis methods, and all the neutral-lossMS/MS spectra show the peptides contain one phosphate group (FIG. 21).

All the MS/MS product ion spectra were analyzed with Sequest in anattempt to assign a phosphorylation site and parent protein to eachpeptide, but this did not result in unambiguous assignments. DuringMS/MS nearly all phosphopeptides underwent neutral loss to a very highdegree with very little residual fragmentation along the peptidebackbone, which is needed to produce spectra of a quality high enoughfor unambiguous assignments. In general backbone fragmentation was atthe same level as chemical noise, obscuring the features needed toidentify the peptides. As noted above, this is a common limitationencountered during MS/MS analysis of peptides containing phosphoserineand phosphothreonine. See e.g., DeGnore et al., supra. Even whenphosphopeptides lose phosphate by neutral loss, the position of thephosphorylation site can be determined as long as there is sufficientresidual backbone fragmentation, because neutral loss leaves an unusualresidue at the phosphorylation site: phosphoserine becomesdehydroalanine, and phosphothreonine becomes dehydroaminobutyric acid.

LC-MS³ Analysis

Some phosphopeptides in this sample were identified by LC-MS³, that is,the neutral-loss ions were subjected to an additional level of MS togive sufficient backbone fragmentation for identification. This processis simpler to implement on ion trap mass spectrometers than on othertypes of mass spectrometers. As peptides elute from the LC system, asurvey MS scan is performed, and MS/MS spectra are collected for thethree most abundant ions, if they are above a pre-set intensitythreshold and if they have not been recently analyzed by MS/MS already.However, if neutral loss of 49, 32.7, or 24.5 is detected during MS/MS,then before collecting another MS/MS spectrum or another survey MS scan,the instrument first isolates the neutral loss ion, fragments it, andmeasures the product ion masses. If the neutral-loss ion no longercontains phosphate, it is more likely to fragment like anon-phosphorylated peptide and give a useful product ion spectrum. Withcertain modifications to the instrument control software, MS³ spectracan be collected in the same data-dependent manner as MS/MS spectra, andthe MS³ spectra can be analyzed further with Sequest. See Tomaino andRush et al., supra.

Data-dependent LC-MS³ was performed on the remainder of the elutedfraction, an 0.8 μl aliquot. FIG. 22 compares the MS/MS spectra (leftpanels) and the MS³ spectra (right panels) for three phosphopeptidesthat were identified by this method. Each MS/MS spectrum containspredominantly one product ion, an intense peak differing from the parention mass by 32.7, consistent with loss of one phosphate from aphosphopeptide ion with a charge of +3. Nearly all other peaks in thespectrum are at least 20-fold less intense than the neutral-loss ion.The MS/MS spectra collected during LC-MS³ analysis of this sample arevery similar to the MS/MS spectra collected during LC-MS/MS analysis,described above, and illustrate how neutral loss can dominate MS/MSspectra of peptides containing phosphoserine or phosphothreonine.Because neutral loss of 32.7 was detected during MS/MS, the massspectrometer automatically subjected the neutral-loss ion to MS³ toproduce the spectra shown in the right panels. These show severalproduct ions of varying intensities distributed throughout the spectra,and as expected they resemble MS/MS spectra of non-phosphorylatedpeptides.

Using Sequest a phosphorylation site and parent protein can be assignedto each of the three MS³ spectra shown in FIG. 22. As noted in FIG. 21,all three of these assigned phosphopeptides correspond to candidatephosphopeptides identified during MALDI-TOF mass spectrometry. Panel 1corresponds to PTN6_HUMAN, residues 576-595, with phosphorylation atSer-585 or Ser-588. Although Sequest unambiguously identified thepeptide, in this example, it could not distinguish the two possiblephosphorylation sites. However, the sites can be distinguished based onthe known specificity of the phospho-(Ser) PKC substrate antibody: thesequence context of Ser-588 (KGS*LK) fits the antibody's specificity butthe sequence context of Ser-585 does not (EKS*KG) [underlined residuesmatch the specificity motif (R/K)XS*(hyb)(R/K)].

PTN6 is protein-tyrosine phosphatase 1c, also known as hematopoieticcell protein-tyrosine phosphatase, relevant because the phosphopeptidesin this experiment were purified from a human cell line derived from anacute T cell leukemia (Jurkat cells). Brumell et al. (J. Biol. Chem.272: 875-882 (1997)) have suggested that this specific tyrosinephosphatase is inhibited by PKC-mediated serine phosphorylation, but thespecific phosphorylation site has not been identified. Presently, themethod of the invention has identified Ser-588 as a possible site ofPKC-mediated serine phosphorylation.

Panels 2 and 3 correspond to two overlapping peptides from UFD1_HUMANthat contain the same phosphorylation site. Sequest assigned residues322-343 with phosphorylation at Ser-335 to the spectrum in panel 2 andresidues 333-343 with phosphorylation at Ser-335 to the spectrum inpanel 3. The longer peptide is related to the shorter peptide byincomplete proteolytic cleavage: Glu-C did not cleave at Glu-332completely. In both cases the quality of the Sequest assignments isgood, and the position of the phosphorylated residue is unambiguous. Thesequence context of Ser-335 (GQS*LR) partially fits the antibody'sspecificity. UFD1 is ubiquitin fusion degradation protein 1. Thisprotein has not been previously shown to be phosphorylated. Presently,the method of the invention has identified Ser-335 as a novelphosphorylation site.

Confirmation of Sequence

For demonstrative purposes, one of the novel phosphorylation sites wasconfirmed by showing a synthetic peptide with the assigned sequence andphosphorylation site gives MS/MS and MS³ spectra that are identical tothe MS/MS and MS³ spectra of the biological peptide, i.e., the peptidepurified by the method of the invention from Glu-C-digested Jurkatcells. UFD1 333-343 phospho-Ser-335 was synthesized at Cell SignalingTechnology using Fmoc chemistry. The full-length peptide was purified byHPLC and then analyzed using the same LC-MS³ method described above.

The MS/MS and MS³ spectra for the biological peptide (top panels) andthe synthetic peptide (bottom panels) are compared in FIG. 23. Portionsof the MS/MS spectra have been amplified by a factor of 10 to show ionsother than the neutral-loss ion more clearly. The correspondence betweenthe MS³ spectra demonstrates that the assigned peptide sequence andphosphorylation site are correct. Even though the quality of the MS/MSspectra is compromised by a dominant neutral-loss ion, there is goodcorrespondence between the minor peaks of the two spectra.

In this example, Sequest assigned a peptide sequence and phosphorylationsite to a spectrum, and the assignment was confirmed by showing asynthetic peptide with that sequence and phosphorylation site gives thesame spectrum. This establishes a formal link between a specificphosphopeptide and its spectrum. This is a simple and convincing way tofurther evaluate marginal Sequest assignments or to confirm assignmentsthat are considered especially important.

Marginal Assignments

As discussed above, neutral loss of phosphate from phosphoserine orphosphothreonine can make it difficult to assign a peptide sequence toan MS/MS spectrum and occasionally assignments will be ambiguous. In aglobal proteomic method, where phosphopeptides are isolated and analyzedseparately from non-phosphorylated peptides, often the only peptide froma particular protein will be the purified phosphopeptide, andunambiguous assignments are likely to be more difficult to achieve.Accordingly, marginal assignments may be of higher value, and may beworth pursuing further. Marginal assignments that are worth furtherinvestigation can be identified by using simple computer programs toscreen the bulk results for assignments that fit the known specificityof the antibody used to isolate the phosphopeptides.

As an example of this, the MS/MS spectra of the sample described herewas further screened for marginal assignments, using antibodyspecificity and our higher-confidence MS³ results as guides. Asdescribed above, MS³ analysis identified two novel phosphorylation sitesin three different peptides: one mapped to PTN6 and fit the knownphospho-(Ser) PKC substrate motif, and the other two mapped to UFD1 andfit the motif partially. A comparison of the peptide sequences showed avariation of the motif might be sufficient for antibody recognition: thePTN6 site contained the sequence S*LKRK, and the UFD1 site contained thesequence S*LRKK. Based on this, all the Sequest output files weresearched, which listed the top 20 candidate peptide sequences for eachspectrum, for marginal results that fit the consensus sequenceS*L(R/K)X(R/K) (SEQ ID NO: 40).

This search found a fourth candidate phosphopeptide in an MS/MSspectrum: BRB1_HUMAN, residues 206-233 with phosphorylation at Ser-228.The sequence contains S*LRTR. This peptide has a mass of 3,297 andcorresponds to a peak observed during MALDI-TOF mass spectrometry(assigned mass 3,294 in FIG. 21). It is a good example of a marginalphosphopeptide assignment: it is the fourteenth-ranked peptide after theinitial round of Sequest scoring, and the eighth-ranked peptide afterthe final scoring round. Although there are higher-ranked peptides afterthe final round, they all received very poor scores in the initialround, where they were ranked ninety-fourth or worse. Nevertheless, thisresult is worth pursuing because the assigned peptide fits theantibody's known specificity and it fits well the higher-confidenceassignments made on the basis of MS³ spectra.

BRB1 is the B1 bradykinin receptor. It is known that the B1 bradykininreceptor activates protein kinase C (see Christopher et al. Hypertension38: 602-605 (2001)). There are no known phosphorylation sites in the B1bradykinin receptor, but the B2 bradykinin receptor is phosphorylated atSer residues in response to activation of protein kinase C (see Blaukatet al. J. Biol. Chem. 276:40431-40 (2001)). Furthermore, protein kinaseC phosphorylation of receptors has been postulated as a generalmechanism for receptor desensitization. It is therefore reasonable topresume that protein kinase C could phosphorylate B1 receptors as well.In addition, it is known that the expression of the BRB1 receptor isupregulated on T cells derived from peripheral blood of patients withmultiple sclerosis, relevant because this phosphopeptide was purifiedfrom a human cell line derived from an acute T cell leukemia (see e.g.,Prat et al. Neurology 53:2087-2092 (1999)). The site of phosphorylationtentatively assigned here is in a domain of the protein that ispredicted to be cytoplasmic. This tentative assignment may be furtherexplored by analyzing a synthetic peptide with the assigned sequence andphosphorylation site as described above.

The ability to filter assignments and extract marginal assignments thatare worth investigating further is a unique advantage of antibody-basedpurification methods. Without use of an antibody and knowledge of theantibody's specificity, these marginal assignments would be overlooked.

EXAMPLE VI Isolation of Peptides Containing the Akt Substrate Motif froman Extract of Cells Expressing Activated Akt Protein Kinase

Peptides containing the Akt substrate motif (RXRXXT*/S*,T*=phosphothreonine, S*=phosphoserine) can be selectively isolated froma complex mixture of peptides, such as a digested cell lysate. The Aktprotein kinase is an important regulator of cell survival and insulinsignaling, but very few of its in vivo targets have been identified.Studies with synthetic peptide substrates of Akt (Alessi et al., FEBSLett. 399: 333-338 (1996)) as well as the analysis of known Aktphosphorylation sites on GSK-3 (Franke et al. Cell 88: 435-437 (1997)),Bad (Pap et al.,

J. Biol. Chem. 273: 19929-19932 (1998), and Caspase-9 (Cardone et al.,Science 282: 1318-1321 (1998)) indicate that Akt phosphorylates itssubstrates only at a serine or threonine in a conserved motifcharacterized by arginine at positions −5 and −3.

Phospho-(Ser/Thr) Akt substrate polyclonal antibody (Cell SignalingTechnology, Inc., product number 9611) is a motif-specific,context-independent antibody that recognizes phosphopeptides with theconsensus substrate motif RXRXX(T*/S*), where R is arginine, X is anyamino acid, and T*/S* indicates phosphothreonine or phosphoserine. Thespecificity of the phospho-(Ser/Thr) Akt substrate antibody is that itbinds preferentially to proteins and peptides that containphosphothreonine or phosphoserine preceded by lysine or arginine atpositions −5 and −3, i.e., (K/R)X(K/R)XX(T*/S*) (SEQ ID NO: 15), in amanner substantially independent of the surrounding amino acid sequence.To identify potential substrates on a genome-wide (cell-wide) basis,immobilized phospho-Akt substrate antibody was used to immunoaffinitypurify phosphopeptides from a proteinaceous preparation in accordancewith the method of the invention, as described below.

For this example, the model system was 3T3 mouse fibroblast cells thathad been stably transfected to express active Akt protein kinaseconstituitively and that had been treated with 50 ng/ml platelet-derivedgrowth factor (PDGF) for 15 minutes. The cells were washed, harvested,and lysed by sonication, proteins in the lysate were denatured, and thelysate was cleared by centrifugation.

To show that activated Akt protein kinase had phosphorylated many targetproteins, the cell extract was analyzed by SDS-PAGE and Western blotting(FIG. 24). Activation of Akt protein kinase was shown by probing a blotof PDGF-treated, transfected cell extract (lane 2) and untreated,untransfected cell extract (lane 1) with Akt antibody (Cell SignalingTechnology, Inc., product number 9272), phospho-Akt (Thr308) antibody(Cell Signaling Technology, Inc., product number 9275), and phospho-Akt(Ser473) antibody (Cell Signaling Technology, Inc., product number9271). This showed that PDGF treatment altered the phosphorylation stateof Akt protein kinase (panels 2 and 3) but not its overall cellularexpression level (panel 1). PGDF treatment also altered thephosphorylation state of a large number of different proteins thatcontain the phospho-Akt substrate motif, shown by probing the blot withphospho-Akt substrate antibody (panel 4). In a separate experiment, itwas shown that the major protein recognized by phospho-Akt substrateantibody after PDGF treatment (the dark band near the bottom of panel 4,lane 2) is the ribosomal protein S6, which is known to be phosphorylatedin response to growth factor treatment (Ferrari and Thomas, Crit. Rev.Biochem. Mol. Biol. 29: 385-413 (1994)).

Proteins in the extract were digested to peptides with endoproteinaseGlu-C immobilized to F7m, a polyvinyl matrix bead (MoBiTec, part numberP5101), and the immobilized Glu-C was removed by centrifugation.Phosphopeptides containing the phospho-Akt substrate motif were purifiedfrom the digest with phospho-Akt substrate antibody immobilized toagarose by hydrazide chemistry, as described above for the P-Tyr-100monoclonal antibody; each milliliter of resin was reacted with 2milligrams of antibody. The Glu-C-digested crude cell extract (about 3.5mg, 0.25 mg/ml protein) was contacted with immobilized phospho-Aktsubstrate antibody-resin (40 μl, 2 μg/μl) in batch format at 4° C. for16 hours, and unbound peptides were removed by centrifugation. Theantibody-resin was washed extensively (four times with 0.5 ml ice-coldPBS and three times with 0.5 ml ice-cold water). Bound peptides werethen eluted with 120 μl 0.1 M glycine, pH 2.3. Before analysis byMALDI-TOF mass spectrometry as described above, a 9 μl portion of theeluted fraction was desalted and concentrated with a reversed-phaseZipTip microcolumn.

MALDI-TOF Analysis

The masses of the peptides that bound to and eluted from the phospho-Aktsubstrate antibody were measured by MALDI-TOF mass spectrometry before(FIG. 25, top panel) and after (bottom panel) treating the peptidefraction with calf intestinal phosphatase, which can remove phosphategroups from phosphopeptides and produce ions with masses 80 lower thanphosphopeptides for each phosphate group in the peptide, to confirm theeluted peptides are phosphorylated. In FIG. 25, peaks labeled with astar correspond to phosphopeptides, peaks labeled with an open circlecorrespond to nonphosphorylated peptides, and peaks labeled with asquare are phosphopeptides that have undergone metastable decompositionand neutral-loss of phosphate.

Four candidate phosphopeptide peaks (FIG. 25, top panel) are eachaccompanied by companion peaks that are broader and apparently 84 lowerin mass, e.g., the peak with a mass of 2,404 has a partner peak at2,320, and likewise 2,334, 2,324, and 2,254 have partner peaks at 2,250,2,241, and 2,171, respectively. These companion peaks correspond tometastable decomposition products of phosphopeptides, formed byneutral-loss of phosphate while the phosphopeptide ions are traveling tothe detector of the mass spectrometer. Metastable decomposition ofphosphopeptides has been noted by others and can be used to recognizeand assign phosphopeptides in a MALDI-TOF mass spectrum (Annan and Carr,Anal. Chem. 68: 3413-21 (1996)). As described in the previous example,it has been observed that some synthetic peptides containingphosphoserine or phosphothreonine but not phosphotyrosine residuesundergo metastable decomposition. The MALDI-TOF mass spectrum in FIG. 25indicates these candidate phosphopeptides probably contain phosphoserineor phosphothreonine, in accordance with the antibody's knownspecificity.

When the bound peptide fraction was treated with calf intestinalphosphatase, 3 of the 4 candidate phosphopeptides gave dephosphorylatedpeptides that were 80 (for one phosphate group) or 160 (for twophosphate groups) lower in mass than the peptides before treatment (FIG.25, bottom panel): 2,404 and 2,324 differ from 2,244 by two or onephosphate groups, respectively, and 2,334 differs from 2,254 by onephosphate group. The presence of metastable decomposition peaks afterphosphatase treatment indicates these peptides are still phosphorylated,i.e., the phosphopeptide with a mass of 2,404 probably contains at leastthree phosphate groups, and the peptide with a mass of 2,334 probablycontains at least two phosphate groups. This is supported by theLC-MS/MS analysis described below, which defined the phosphate contentof these peptides more precisely.

It is believed that two of the four immunoaffinity-purified peptides(FIG. 25, top panel) correspond to a known phosphopeptide from theribosomal protein S6 (accession number P10660), which is the majorprotein in the PDGF-treated cell extract recognized by Western blottingwith phospho-Akt substrate antibody (FIG. 24): the phosphopeptides withan observed mass of 2,254.5 and 2,334.4 fit the expected mass for theGlu-C-peptide from S6 protein QIAKR RRLSS LRAST SKSE (SEQ ID NO: 41)with 1 and 2 phosphate groups, respectively (calculated protonatedpeptide masses of 2,254.2 and 2,334.2). Based on the duration of PDGFtreatment in this experiment and published reports on the order ofphosphorylation (Ferrari et al. J. Biol. Chem. 266: 22770-5 (1991)), itis expected that only 2 of the 5 phosphorylation sites in this peptideare phosphorylated, Ser235 and Ser236, underlined in the peptidesequence shown above. Furthermore these two sites in the peptide fit theknown specificity of the phospho-Akt substrate antibody: Ser235 fitsKXRXXS*, and Ser236 fits RXRXXS*.

LC-MS/MS Analysis

The peptides that bound to and eluted from the phospho-Akt substrateantibody were further analyzed by LC-MS/MS. A 25 μl portion of thepeptide fraction was desalted and concentrated with a reversed-phaseZipTip microcolumn and eluted with 2 μl 0.1% trifluoroacetic acid, 40%acetonitrile. An 0.4 μl aliquot of the eluted fraction was mixed with anACHA matrix solution and analyzed by MALDI-TOF mass spectrometry, and itgave a spectrum similar to the one shown in FIG. 25. The remainder ofthe eluted fraction was analyzed by LC-MS/MS.

LC-MS/MS analysis was performed as described above (Example IV). Thechromatogram obtained by analyzing this sample is shown in FIG. 26. Thefirst panel of FIG. 26 shows where survey MS scans were collected, andthe second panel shows where MS/MS spectra were collected. The third,fourth, and fifth panels show where neutral loss of 49, 32.7, and 24.5,respectively, was detected, characteristic of ions with charges of +2,+3, and +4 that have undergone neutral loss of phosphate. The occurrenceand intensities of neutral-loss ions are plotted in the third, fourth,and fifth panels of FIG. 26 to help locate candidate phosphopeptides.The neutral loss plots show that phosphopeptide candidates tend to eluteearly in the chromatogram, as expected for phosphopeptides due to thehydrophilicity of phosphate groups, and that neutral loss is observed inmany of the MS/MS spectra, suggesting this sample is highly enrichedwith phosphopeptides.

As noted earlier, neutral loss during MS/MS is the same process asmetastable decomposition during MALDI-TOF mass spectrometry. Asexpected, many of the phosphopeptides showing neutral loss duringLC-MS/MS (FIG. 26, panels 3-5) are the same phosphopeptides that gavemetastable decomposition during MALDI-TOF mass spectrometry+(FIG. 25,top panel), see FIG. 27. Most peptides showing neutral loss during MS/MScontained more than one phosphate group. The MS/MS spectra often gave aclear indication of the number of phosphate groups present in eachpeptide ion, which MALDI-TOF mass analysis did not provide even aftertreating the peptides with phosphatase.

The phosphopeptide from the ribosomal protein S6 was observed with one,two, and three phosphates, in good agreement with the MALDI-TOF resultsdescribed above. FIG. 28 shows a portion of the MS/MS spectra for the S6phosphopeptide with 1 (panel 1), 2 (panel 2), or 3 (panel 3) phosphates,the parent ions for all three spectra have a charge of +3. Panel 1 showsthe spectrum of a parent ion with an m/z value of 752.51 undergoingneutral loss to give a product ion with an m/z value of 719.86, adifference of 32.65, close to the theoretical m/z difference of 32.66for loss of 98 from an ion with a charge of +3. Only one loss of thism/z value is detected, that is, a product ion corresponding to loss oftwo phosphate groups (m/z of 687.20) is not detected. On this basis themass of the peptide is 2,254.5, and it contains 1 phosphate group.Similarly panel 2 shows product ions that have lost this m/z value onceand twice, allowing assignment of two phosphate groups, and panel 3shows loss one, two, and three times, corresponding to 3 phosphategroups. In agreement with this the parent ion masses increase by 80 foreach additional phosphate group. As expected, the phosphopeptides elutedearlier during reversed-phase HPLC as the phosphate content increased:with 3, 2, or 1 phosphate groups the peptide eluted at 7.3, 7.6, and 7.8minutes respectively.

Like this group of ribosomal protein S6 phosphopeptides, LC-MS/MSanalysis showed there may be a second group of related phosphopeptides,labeled “peptide A” in FIG. 27. The observed masses are 2,324.5 (withtwo phosphate groups) and 2,404.6 (with three phosphate groups).

All the MS/MS product ion spectra were analyzed with Sequest in anattempt to assign a parent protein and phosphorylation site to eachpeptide. This did not result in unambiguous assignments because of thehigh level of neutral loss with very little residual fragmentation alongthe peptide backbone. At present, this type of multiply-phosphorylatedsample cannot be analyzed effectively by LC-MS³ using the currentlyavailable version of the software. The current data-dependentacquisition software isolates and fragments the most abundantneutral-loss ion; for multiply phosphorylated peptides this correspondsto the peptide with one phosphate removed by neutral loss, leaving oneor more phosphate groups to undergo neutral loss during MS³. Theacquisition software is being revised (per personal communication) torecognize multiples of neutral loss and to isolate and fragment the ionwith the highest level of neutral loss, even if it is not the mostintense product ion. For example for the spectrum in panel 2 of FIG. 28,the current software would select for MS³ analysis the ion with an m/zvalue of 746.33 because it is the most intense neutral-loss ion; but therevised software will select the ion with an m/z value of 713.87 becauseit shows a higher level of neutral loss. It is expected that furtheranalysis of this sample with revised acquisition software will allow theparent proteins and phosphorylation sites of some of these peptides tobe unambiguously assigned.

Even without unambiguous fragmentation spectra, the tentative assignmentof some of these peptides to a phosphopeptide from the ribosomal proteinS6 is consistent with Western blotting results, which suggest S6 is themajor phosphoprotein detected by phospho-Akt substrate antibody, and theobserved masses and phosphate contents agree with published reports onphosphorylation of this protein after treatment with growth factors.

EXAMPLE VII Isolation of Peptides Containing the 14-3-3 Binding Motiffrom an Extract of Cells Treated with a Cyclic AMP Analog and Insulin

The method of the invention was further employed to isolatephosphopeptides containing a 14-3-3 binding motif from a complex mixtureof peptides existing in a digested cell lysate. The 14-3-3 proteinsregulate several biological processes through phosphorylation-dependentprotein-protein interactions. A phosphoserine-containing consensussequence, motif #1, (R/K)SXS*XP, is present in some binding partners of14-3-3 proteins. Many protein kinases such as Akt and cAMP-dependentprotein kinase (PKA) can phosphorylate this motif to initiate binding of14-3-3 proteins.

Phospho-(Ser) 14-3-3 binding motif monoclonal antibody (4E2) (CellSignaling Technology, Inc., product number 9606) is a motif-specific,context-independent antibody that recognizes phosphopeptides containingconsensus binding motif #1. This antibody is highly specific forpeptides and proteins that contain the consensus motif (R/K)XXS*XP,where R is arginine, P is proline, X is any amino acid, and S* indicatesphosphoserine. This antibody weakly cross-reacts with analogoussequences containing phosphothreonine instead of phosphoserine in thismotif. This antibody was used to immunoaffinity purify phosphopeptidesthat contain motif #1 from a proteinaceous preparation, so as toidentify proteins that may be previously unrecognized binding partnersof 14-3-3 proteins.

For this example, the model system was COS-1 cells, a cell line derivedfrom transformed monkey kidney cells, that had been treated with insulinand 8-(4-chlorophenylthio)-cAMP (cpt-cAMP). Insulin induces the Aktprotein kinase, and the membrane-permeable, metabolically stable cAMPanalog induces the PKA kinase. The induced kinases will phosphorylatemany protein sites, and among these many will be 14-3-3 binding sites,that is, some proteins will become binding partners of 14-3-3 proteinsas a result of phosphorylation by the Akt, PKA, and other inducedprotein kinases. A culture of COS-1 cells was treated with 1 μg/mlinsulin and 1 mM 8-(4-chlorophenylthio)-cAMP (cpt-cAMP) for 10 minutes.The cells were washed, harvested, and lysed by sonication, proteins inthe lysate were denatured, and the lysate was cleared by centrifugation.

To show that treatment with insulin and the cyclic AMP analog had causedan increased level of protein phosphorylation at potential 14-3-3binding sites, the cell extract was analyzed by SDS-PAGE and Westernblotting (FIG. 29). Probing the treated cell extract (lane 2) and theuntreated cell extract (lane 1) with phospho-(Ser) 14-3-3 binding motifantibody (Cell Signaling Technology, Inc., product number 9606) showedthat this treatment altered the phosphorylation state of a significantnumber of different proteins that contain the 14-3-3 binding motif #1.

Proteins in the extract were digested to peptides with endoproteinaseGlu-C immobilized to F7m, a polyvinyl matrix bead (MoBiTec, part numberP5101), and the immobilized Glu-C was removed by centrifugation.Immobilized phospho-(Ser) 14-3-3 binding motif monoclonal antibody (4E2)was prepared as described in Example IIB and was found to contain 4 mgantibody per ml of resin.

Phosphopeptides containing the 14-3-3 binding motif were purified fromthe Glu-C-digested crude cell extract with phospho-(Ser) 14-3-3 bindingmotif monoclonal antibody bound protein G-agarose resin. The digest(about 12 mg, 0.5 μg/μl protein) was contacted with immobilizedantibody-resin (40 μl, 4 μg/μl) in batch format at 4° C. for 16 hours,and unbound peptides were removed by centrifugation. The antibody-resinwas washed extensively (three times with 1 ml ice-cold PBS and two timeswith 1 ml ice-cold water). Bound peptides were then eluted with 150 μl0.1% trifluoroacetic acid, and the eluted peptides were separated fromeluted antibody by centrifugation through a Microcon YM-10 membrane(Millipore, product number 42407), which retains molecules withmolecular weights above 10,000. Before analysis by MALDI-TOF massspectrometry, a 9 μl portion of the YM-10 flow-through fraction wasdesalted and concentrated with a reversed-phase ZipTip microcolumn.

MALDI-TOF Analysis

The masses of the peptides that bound to and eluted from thephospho-(Ser) 14-3-3 binding motif antibody were measured by MALDI-TOFmass spectrometry (FIG. 30). In FIG. 30, peaks labeled with a starcorrespond to phosphopeptides, and peaks labeled with a square arephosphopeptides that have undergone metastable decomposition andneutral-loss of phosphate.

Metastable decomposition showed that the antibody-purified peptidefraction contains several candidate phosphopeptides with phosphoserineor phosphothreonine, as expected based on the antibody's specificity.Metastable decomposition arises when phosphopeptide ions undergoneutral-loss of phosphate while traveling toward the instrument'sdetector and is indicated in MALDI-TOF spectra by the presence of broadcompanion peaks about 84 lower in mass than intact phosphopeptide ions.As noted in Examples V and VI, experience with synthetic peptidesindicates metastable decomposition is a specific and reliable indicatorof peptides that contain phosphoserine or phosphothreonine, so theappearance of metastable decomposition in this spectrum fits the knownspecificity of the antibody used for purification.

A comparison of the MALDI-TOF mass spectrum for this sample (FIG. 30)and the Akt substrate sample described in Example VI (FIG. 19) showsthere may be some overlap between the two sample sets. This is expectedbecause, for both samples, the Akt protein kinase was induced and forboth samples the specificities of the antibodies used for phosphopeptidepurification overlap [(R/K)XX(S*)XP for the phospho-(Ser) 14-3-3 bindingmotif monoclonal antibody 4E2 versus (R/K)X(R/K)XX(S*/T*) for thephospho-(Ser/Thr) Akt substrate motif polyclonal antibody]. Two peptidesthat the sample sets may have in common correspond to the Glu-C peptidefrom the ribosomal protein S6, QIAKR RRLSS LRAST SKSE (SEQ ID NO: 41)with 1 phosphate group and with 2 phosphate groups (see FIG. 27). Ser235and Ser236, underlined in the peptide sequence shown above, fit the Aktsubstrate motif fully and the 14-3-3 binding site motif partially.

LC-MS/MS Analysis

The peptides that bound to and eluted from the phospho-(Ser) 14-3-3binding motif antibody were further analyzed by LC-MS/MS. A 20 μlportion of the peptide fraction was desalted and concentrated with areversed-phase ZipTip microcolumn and eluted with 2 μl 0.1%trifluoroacetic acid, 40% acetonitrile. An 0.4 μl aliquot of the elutedfraction was mixed with an ACHA matrix solution and analyzed byMALDI-TOF mass spectrometry, and it gave a spectrum similar to the oneshown in FIG. 30. The remainder of the eluted fraction was analyzed byLC-MS/MS.

LC-MS/MS analysis was performed as described above (Example IV). Thechromatogram obtained by analyzing this sample is shown in FIG. 31. Thefirst panel of FIG. 31 shows where survey MS scans were collected, thesecond panel shows where MS/MS spectra were collected, and the third,fourth, and fifth panels show where neutral loss of 49, 32.7, and 24.5,respectively, was detected, characteristic of ions with charges of +2,+3, and +4 that have undergone neutral loss of phosphate. The occurrenceand intensities of neutral-loss ions are plotted in the third, fourth,and fifth panels of FIG. 31 to help locate candidate phosphopeptides.The neutral loss plots show that phosphopeptide candidates tend to eluteearly in the chromatogram, as expected for phosphopeptides due to thehydrophilicity of phosphate groups, and that neutral loss is observed inmany of the MS/MS spectra, suggesting this sample is highly enrichedwith phosphopeptides.

Many of the phosphopeptides showing neutral loss during LC-MS/MS (FIG.31, panels 3-5) are the same phosphopeptides that gave metastabledecomposition during MALDI-TOF mass spectrometry (FIG. 30), see FIG. 32.Like the Akt substrate sample described in Example VI, most peptidesshowing neutral loss during MS/MS contained more than one phosphategroup. The LC-MS/MS analysis results support the interpretation made onthe basis of the MALDI-TOF mass spectrum, that there is likely to beconsiderable overlap between the set of peptides purified with the Aktsubstrate antibody and the 14-3-3 binding motif antibody, including thetentatively assigned multiply phosphorylated peptides from ribosomalprotein S6.

Another indication of overlap between the two sample sets is provided byresidual backbone fragmentation observed in some of the MS/MS spectra,see FIG. 33. The left panels are MS/MS spectra from the Akt substrateantibody sample set, and the right panels are the corresponding spectrafrom the 14-3-3 binding motif antibody sample set. The top panels areboth assigned tentatively to an ion with a charge of +4 corresponding tothe S6 peptide with two phosphate groups: in addition to neutral loss,both spectra show a product ion with an m/z value of 668.2, possibly theb17-H₃PO₄ product ion with a charge of +3 (calculated m/z of 668.04).The bottom panels are both assigned to an ion with a charge of +4 thathas a mass of 3,204 and contains two phosphate groups: both spectra showa product ion with an m/z value of 990.7.

All the MS/MS product ion spectra were analyzed with Sequest in anattempt to assign a phosphorylation site and parent protein to eachpeptide. In many cases here (as also noted in Examples V and VI) thisdid not result in unambiguous assignments because of the high level ofneutral loss with very little residual fragmentation along the peptidebackbone. MS/MS showed that many of the most abundant phosphopeptidesare multiply-phosphorylated and will be amenable to MS³ analysis afterthe current data acquisition software is revised to recognize multiplesof neutral loss and to isolate and fragment the ion with the highestlevel of neutral loss (as noted in Example VI).

One peptide in this sample that was unambiguously identified is aphosphoserine-containing peptide from heat shock 27 kDa protein (FIG.34). The residue identified as a phosphorylation site by this method,Ser-78, is known to be phosphorylated by several protein kinases,including S6 kinases and mitogen-activated protein kinases, which arelikely to have been activated by the treatments used to prepare thissample. See e.g., Landry et al. J. Biol. Chem. 267: 794-803 (1992) andBird et al. FEBS Lett. 338: 31-36 (1994). This phosphopeptidecorresponds to a prominent peak detected during MALDI-TOF massspectrometry, labeled “2,384.6” in FIG. 30. The MS/MS spectrum for thepeptide as an ion with a charge of +2 shows a prominent neutral-lossproduct ion, consistent with loss of one phosphate group (see FIG. 32).The spectrum that could be assigned a parent protein and phosphorylationsite by Sequest was produced from the same peptide as an ion with acharge of +3. As expected, the sequence context of Ser-78 (RALS*RQ) fitsthe known specificity of the phospho-(Ser) 14-3-3 binding motif antibodyused to purify the phosphopeptide [underlined residues match thespecificity motif (R/K)XXS*XP].

EXAMPLE VIII Isolation of Peptides Containing the Phospho-PDK1 DockingMotif from a Crude Cell Extract

Peptides containing the phospho-PDK1 docking motif (FXXF(S*/T*)(F/Y)(SEQ ID NO: 42), where F is phenylalanine, X is any amino acid, S*/T*indicates phosphoserine or phosphothreonine, and F/Y indicatesphenylalanine or tyrosine) may be selectively isolated from a complexmixture of peptides, such as a digested cell lysate. Many proteinkinases contain this docking motif sequence, and phosphorylation of thissequence is required for these kinases to bind to3-phosphoinositide-dependent kinase 1 (PDK1). PDK1 plays a central rolein the activation of several growth factor-induced protein kinases,including protein kinase B (PKB), p70 S6 kinase, several PKC isotypes,and serum and glucocorticoid-induced kinase (SGK). See, e.g. Belham etal., Curr. Biol. 11: R93-R96 (1999).

The phospho-PDK1 docking motif 18A2 (bulky rings) monoclonal antibody(Cell Signaling Technology, Inc., product number 9634) is amotif-specific, context-independent antibody that recognizesphosphopeptides with the consensus sequence FXXF(S*/T*)(F/Y), where F isphenylalanine, X is any amino acid, S*/T* indicates phosphoserine orphosphothreonine, and FN indicates phenylalanine or tyrosine. Toidentify other proteins with this PDK1 docking motif or profile theactivation states of known PDK1 substrates on a cell-wide basis,immobilized PDK1 docking motif (bulky rings) antibody may be employed toimmunoaffinity purify phosphopeptides containing the motif from acomplex mixture of peptides, such as a digested cell lysate. Forexample, a proteinaceous preparation may be obtained from a COS cellline (monkey) that overexpresses Akt protein, from 3T3 cells (mouse)treated with platelet derived growth factor, or from Jurkat (human)cells. The extract is prepared and proteins denatured as described above(see “Proteinaceous preparations”), then digested with immobilizedtrypsin or other proteases.

Phosphopeptides containing the PDK1 docking motif are isolated from thecomplex mixture in the digested cell lysate with the bulky ringsmonoclonal antibody (PDK1 docking motif) immobilized to agarose resin byhydrazide chemistry, as described above for P-Tyr-100 monoclonal andP-Thr polyclonal antibodies. The digest is contacted with theantibody-resin in batch format at 4° C. for 1 to 16 hours. Unboundpeptides are then removed by centrifugation, and the antibody-resin isextensively washed before eluting bound peptides with 0.1 M glycine, pH2.3. The eluted peptides are concentrated and desalted withreversed-phase ZipTip microcolumns. The masses of the eluted peptidesare measured before and after treating aliquots of the eluted peptideswith phosphatase, which can remove phosphate groups from thephosphopeptides and reduce the phosphopeptide masses by 80 for eachphosphate present in the peptide. The mixture of phosphopeptides is thenanalyzed by MS/MS, as described above, to obtain partial peptidesequence information to facilitate identifying the parent proteins fromwhich each phosphopeptide originated. It is expected that eachphosphopeptide sequence will fit the PDK1 docking motif consensussequence described above.

EXAMPLE IX Isolation of Acetyl-lysine-Containing Peptides from a CrudeCell Extract

Peptides containing acetylated residues, e.g. acetylated-lysine, may beselectively isolated from a complex mixture of peptides, such as adigested cell lysate, according to the method of the invention. It isknown that acetylation regulates chromatin structure and gene activitythrough modification of histones and transcription factors, and thusspecific isolation of acetylated peptides would provide importantinformation on the activation states of these biologically importantproteins.

Acetylated-lysine monoclonal antibody (Cell Signaling Technology, Inc.,product number 9681) specifically recognizes proteins that have beenpost-translationally modified by acetylation at lysine epsilon-aminogroups. To identify other sites of acetylation, immobilizedacetylated-lysine antibody may be used to immunoaffinity purify modified(i.e. acetylated) peptides from a proteinaceous preparation, accordingto the method of the invention. For example, a digested cell lysatecontaining a complex mixture of peptides may be prepared from a COS cellline (monkey) that overexpresses the HIV Nef protein, which isacetylated at lysine-4. The proteinaceous preparation is prepared andproteins denatured as described above (see “Proteinaceouspreparations”), and digested with immobilized trypsin or other suitableimmobilized proteases that can be removed from the digest bycentrifugation.

Acetylated peptides may then be isolated from the digested cell lysatewith the acetyl-lysine specific antibody (a generalmodification-specific antibody) linked to agarose resin using ahydrazide chemistry, as was described above for the P-Tyr-100 monoclonalantibody and the P-Thr-polyclonal antibody. To isolate acetylatedpeptides, the digested crude extract may then be contacted with theimmobilized acetylated-lysine monoclonal antibody at 4° C. overnight.The resin may then be recovered by centrifugation and extensively washedas described above. The bound peptides may then be eluted by treatingthe antibody-resin with an eluting solvent such as 0.1% trifluoroaceticacid and centrifugation through a plastic frit.

For this cell line, the overexpressed HIV Nef protein is the mostprominent acetylated protein in the cell, and it is expected thatacetylated HIV Nef peptides will be specifically isolated, along withother acetylated peptides, according to the method of the invention.These peptides and other acetylated peptides may be further analyzed byMS/MS to obtain partial sequences that can be used to identify theparent proteins. For the HIV Nef protein, for example, a partialsequence will help confirm the peptide isolated from the crude extractis indeed from the HIV Nef protein. Analysis of other acetylatedpeptides purified by this method may identify new, previously unknownacetylation sites, and in these cases the partial sequence analysis isnecessary to match each acetylated peptide with its parent protein.Generally, a peptide's mass and a partial sequence of that peptide issufficient to identify the parent protein for that peptide, as long asthe parent protein's sequence is stored in a public protein sequencedatabase. See Mann et al., Anal. Chem. 66:4390-4399 (1994).

EXAMPLE X Profiling of Activated Pathways in Tumor Tissue by Isolationof Modified Peptides from a Crude Tissue Extract

Activation status of important biological signaling pathways in diseasedtissue may be profiled by selective isolation of modified peptides inaccordance with the method of the invention. Activation of specificcellular signaling pathways depends, for example, upon thephosphorylation of specific proteins. Therefore, protein phosphorylationstates in target cell, e.g. tumor cells, may be used to profile pathwayactivation by preparing cell extracts from biopsy samples of tumortissues from which modified peptides may be selectively isolated.

Profiling of protein phosphorylation states in tumor cell, e.g. a breasttumor cell, may be carried out by obtaining a proteinaceous preparation,which contains a complex mixture of peptides, from the target tumorcell. A proteinaceous preparation may be obtained from a single needlebiopsy from a breast tumor, which provides sufficient cellular extractto profile the activation status of multiple signaling pathways,including, e.g., the MAP kinase pathway, various growth factor receptorpathways, including epidermal growth factor receptor, steroid receptors,such as the estrogen receptor, and the PI-3-kinase Akt pathway. All ofthese pathways have been shown to be involved in breast cancer and areimportant targets for current and future drug development and patienttherapy.

To evaluate changes in the signaling pathways of specific breast cancerbiopsies, a proteinaceous preparation is obtained from the biopsy sampleand desired modified peptides, e.g. phosphopeptides, from that fractionare immunoaffinity purified and characterized by MS as described above.A protein fraction is obtained from frozen biopsy tissue by sonication,and insoluble material and cytoskeletal proteins are removed bycentrifugation. The supernatant fraction, containing the bulk of thecellular proteins, is then denatured by heat treatment and digested withimmobilized trypsin or some other specific proteolytic enzyme. Thisproteinaceous preparation contains modified phosphopeptides frommultiple different proteins. The proteinaceous preparation is contactedwith an immobilized general phospho-specific antibody, e.g. aphosphotyrosine-specific antibody, to isolate phosphopeptides from thecomplex mixture in the proteinaceous preparation by immunoaffinityisolation. A single type of antibody-resin or several types ofantibody-resin in series may be employed; e.g., the protein fraction iscontacted with an immobilized phosphotyrosine-specific antibody (e.g. ina column, as previously described), and the unbound fraction from thatstep is then treated with an immobilized Akt substrate motif-specificantibody in a second support, etc. The immobilized antibody-resins arewashed extensively to remove unbound (e.g. nonphosphorylated) peptides,and the bound peptide fraction is then recovered by treating theantibody-resin with an eluting solvent such as 0.1% trifluoroaceticacid.

The eluted phosphopeptides are then analyzed by MALDI-TOF MS, andphosphorylation is confirmed by measuring the peptide mass again aftertreating an aliquot of the bound fraction with phosphatase, which shouldreduce each peptide mass by 80 for each phosphate group. To assign themodified peptides to their parent proteins, the bound peptide fractionis analyzed by MS/MS. The partial sequence information obtained, alongwith the peptide mass, is sufficient to unambiguously identify theparent protein of each peptide. See Mann et al. (1994), supra. Ideally,this procedure is performed with tumor and normal cell biopsies from thesame patient. However, if certain phosphorylation sites are known to bediagnostic markers for a specific cancer, then the method can be used toassay the presence of those markers only, without a normal cellreference.

The amounts of phosphorylated peptides isolated from the target cellsfrom tumor tissues are compared to levels observed in extracts fromreference cells from normal tissues. Alterations in phosphorylation of agiven peptide (and thus, its parent protein), when compared to thereference cell phosphorylation state, will indicate activation of thecorresponding signaling pathway. Information obtained from thisprofiling may be used to determine the best therapy for the patient, aswell as to monitor the specific effects of the therapy, e.g. drugtreatment, on the targeted signaling pathways. Profiling ofphosphorylation states in a target diseased cell, such as a breast tumorcell, also provides information useful in drug development, e.g. toassess the effect of a test drug, as well as for cancer research toidentify which signaling proteins and pathways are involved in specificcancers. Other post-translational modifications of proteins that may berelevant to disease states, such as cancer, may similarly be examined bythe methods disclosed herein.

EXAMPLE XI Purification and Identification of Phosphotyrosine Peptidesfrom Anaplastic Large Cell Lymphoma Cell Lines

The method of the invention was employed to identify tyrosinephosphorylated peptides from two cancer cell lines that express the sameactivated tyrosine kinase. Karpas 299 and SU-DHL-1 are derived fromanaplastic large cell lymphomas (ALCL). The majority of ALCL ischaracterized by the presence of the t(2;5)(p23;q35) chromosomaltranslocation that causes the fusion of the nucleophosmin and anaplasticlymphoma kinase (ALK) genes. See Morris et al. Science 263:1281-1284(1994). Although the two cell lines are derived from different patients,both express the oncogenic fusion kinase NPM-ALK, which possessesconstitutive tyrosine kinase activity and can transform non-malignantcells.

Lysates were prepared from 2×10⁸ cells for both cell lines and digestedin 2 M urea with trypsin after treatment with DTT and iodoacetamide toalkylate cysteine residues. Before the immunoaffinity step, peptideswere prefractionated by reversed-phase solid phase extraction usingSep-Pak C₁₈ columns (1 ml column volume per 2×10⁸ cells) to separatepeptides from other cellular components. The solid phase extractioncartridges were eluted with steps of 5, 15, 25, and 40% acetonitrile.Each lyophilized peptide fraction was redissolved in 1 ml PBS andtreated with phosphotyrosine antibody (P-Tyr-100, CST #9411) immobilizedon protein G-Sepharose (Roche) (60 μg antibody, 15 μl resin) overnightat 4° C. Antibody-resin was thoroughly washed, andimmunoaffinity-purified peptides were eluted with 75 μl of 0.1% TFA. Aportion of this fraction (40 μl) was concentrated with Stage tips andanalyzed by LC-MS/MS, using a ThermoFinnigan LCQ Deca XP Plus ion trapmass spectrometer. Peptides were eluted from a 10 cm×75 μmreversed-phase column with a 45-min linear gradient of acetonitriledelivered at 280 nl/min. MS/MS spectra were evaluated using the programSequest with the NCBI human protein database.

This revealed a total of 117 tyrosine phosphorylation sites in SU-DHL-1and 84 tyrosine phosphorylation sites in Karpas 299. As expected therewas large overlap (72%) between the phosphorylation sites found in thesetwo similar cell lines. Some phosphotyrosine sites found in the ALCLcell lines that originate from known cell signaling proteins are shownin Table 6. TABLE 6 Phosphotyrosine peptides found in ALCL cell linesProtein Name‡ K§ S§ Sequence Tyrosine kinase   activated p21cdc42Hs •KPTpYDPVSEDQDPLSSDFK   kinase   anaplastic lymphoma • HQELQAMQMELQSPEpYK  kinase   anaplastic lymphoma • • TSTIMTDpYNPNpYCFAGK   kinase  anaplastic lymphoma • GLGHGAFGEVpYEGQVSGMPND   kinase PSPLQVAVK  anaplastic lymphoma • • NKPTSLWNPTpYGSWFTEK   kinase   anaplasticlymphoma • • HFPCGNVNpYGYQQQGLPLEAA   kinase TAPGAGHYEDTILK   Januskinase 3 • • DLNSLISSDpYELLSDPTPGAL APR Ser/Thr kinase   cdc2 • •IGEGTpYGVVYK   cdc2 • • IGEGTYGVVpYK   DYRK1A • • VYNDGYDDDNpYDYIVK *DYRK1A • • IYQpYIQSR   DYRK3 • pYEVLKIIGKGSFGQVAR * ERK2 •VADPDHDHTGFLTEpYVATR * GSK3 alpha • • GEPNVSpYICSR * HIPK1 •AVCSTpYLQSR * p38 alpha MAPK • • HTDDEMTGpYVATR * PRP4K • •LCDFGSASHVADNDITPpYL VSR Adaptor   CD2-associated • ISTpYGLPAGGIQPHPQTK  protein   dok2 • GQEGEpYAVPFDAVAR   HGF reg. tyr. • VCEPCpYEQLNR  kinase subs.   insulin receptor • LEpYYENEK   substrate 1   insulinreceptor • VDPNGpYMMMSPSGGCSPDIGG   substrate 1 GPSSSSSSSNAVPSGTSYGK  intersectin 2 • REEPEALpYAAVNK   isoform 1   Oncogene CBL2 • •IKPSSSANAIpYSLAAR   SHC • • MAGFDGSAWDEEEEEPPDHQpY pYNDFPGK   SHC • •ELFDDPSpYVNVQNLDK   SHP2 • • IQNTGDpYYDLYGGEK   T lymphocyte •SCQNLGpYTAASPQAPEAASST   adaptor GNAER   T lymphocyte • SQDPNPQpYSPIIK  adaptor   T lymphocyte • GSPGEAPSNIpYVEVEDEGLPA   adaptor TLGHPVLR  Wiskott-Aldrich • LIpYDFIEDQGGLEAVR   syn. protein‡ * indicates activation loop peptides.§ “K” indicates peptide found in Karpas 299, “S” in SU-DHL-1.• indicates phosphopeptides found in Karpas 299 or SU-DHL-1.

To identify more phosphorylation sites, the same SU-DHL-1 cell extractwas digested with trypsin, chymotrypsin, endoproteinase GluC, orelastase, and tyrosine phosphorylated peptides were purified andanalyzed as described above, resulting in the identification of 90phosphotyrosine peptides from the trypsin digest, 58 from chymotrypsin,43 from endoproteinase GluC, and 82 from elastase. A panel of proteasesincreased the number of distinct tyrosine phosphorylation sites foundfrom 88 using trypsin alone to 197 using all four proteases. Most (35 of54) phosphorylation sites from the elastase digest were not found in thetryptic digest. This small union between phosphorylation sites from twodigests shows that the use of different proteases produced a morecomplete phosphorylation profile. Activation loop phosphorylation atTyr-1282 of ALK was found only after digestion with chymotrypsin, as a12-residue peptide; this residue is predicted to be in a 5-residuetryptic peptide or a 57-residue endoproteinase GluC peptide, bothoutside the range of peptide lengths amenable to MS/MS-basedidentification. In addition, the protease panel generated overlappingphosphopeptide sequences, which confirmed phosphorylation siteassignments. The ALK Tyr-1507 site was found in five peptides: threetryptic peptides, one chymotryptic peptide, and one elastase peptide.

A total of 264 phosphopeptides representing 197 differentphosphotyrosine sites were identified in SU-DHL-1 cells. The onlytyrosine kinase showing activation loop phosphorylation in the ALCL celllines was ALK. Altogether nine different sites of ALK phosphorylation,including five new sites, were observed. The four known ALK sitesincluded phosphotyrosine residues that allow ALK to interact with othersignaling proteins such as phospholipase C-gamma, SHC, and IRS-1. Amonghuman lymphomas, STAT3 phosphorylation is correlated with ALKexpression, suggesting STAT3 phosphorylation may be a secondary markerfor this malignancy, and a recent study demonstrated a favorableclinical outcome for the minority of ALCL patients who have tumors thatexpress ALK but not phosphorylated STAT3. These ALCL cell lines werefound to contain both STAT3 isoform 1 and STAT3 isoform 2 phosphorylatedat Tyr-705, which induces dimerization and nuclear translocation of thistranscription factor.

EXAMPLE XII Purification and Identification of Phosphotyrosine Peptidesfrom Pervanadate-Treated Jurkat Cells

Tyrosine phosphorylated peptides were identified frompervanadate-treated Jurkat cells according to the method of theinvention. Jurkat cells are an established T cell line derived frompatients with acute lymphoblastic leukemia and leukemic transformednon-Hodgkin lymphoma. Pervanadate produces a hyperphosphorylated cellstate by disabling protein tyrosine phosphatases, markedly increasingthe level of protein-associated phosphotyrosine. See Srivastava andSt-Louis, Mol. Cell. Biochem. 176: 47-51 (1997). Proteins were extractedfrom 2×10⁸ cells under denaturing conditions and digested with trypsin,and the resulting complex peptide mixture was separated from non-peptidecomponents, concentrated, and partitioned into three fractions byreversed-phase solid-phase extraction. Each fraction was then treatedwith the phosphotyrosine-specific antibody P-Tyr-100 immobilized onagarose beads. After thorough washing, peptides were eluted from theimmobilized antibody with dilute acid and analyzed by nanoflow LC-MS/MSusing an ion trap mass spectrometer. MS/MS spectra were assigned topeptide sequences using the program Sequest, and each assignment wasmanually confirmed.

A total of 175 phosphorylation sites in 156 phosphotyrosine peptides wasfound in this sample. Most of the purified peptides were phosphorylated:88 of the 100 top-scoring Sequest assignments corresponded tophosphotyrosine peptides. Unphosphorylated peptides were usuallyhydrophobic and from abundant proteins, and it is likely theycontaminated the phosphopeptide fractions because of a non-specificaffinity for agarose beads. Some of the phosphopeptides originating fromcell signaling proteins that were found in this sample are listed inTable 7. TABLE 7 Phosphotyrosine peptides found in pervanadate-treatedJurkat cells Protein Name‡ TCR Sequence Tyrosine kinase * ephrinreceptor EphA4 VLEDDPEAApYTTR * fer tyrosine kinase QEDGGVpYSSSGLK  oncogene LCK Yes NLDNGGFpYISPR * oncogene LCK Yes LIEDNEpYTAR  oncogene LCK Yes SVLEDFFTATEGQpYQPQP   ZAP-70 Yes IDTLNSDGpYTPEPAR  ZAP-70 Yes PMPMDTSVpYESPpYSDPEELK * ZAP-70 Yes ALGADDSpYpYTAR Ser/Thrkinase   cdc2 IGEGTpYGVVYK   cdk6 ADQQpYECVAEIGEGApYGK * GSK3 alphaGEPNVSpYICSR   myosin light chain QEGSIEVpYEDAGSHpYLCLLK   kinase 1 *p38 alpha MAPK Yes HTDDEMTGpYVATR   kinase 1 * PRP4KLCDFGSASHVADNDITPpYL VSR Adaptor   abl-interactor 1TLEPVKPPTVPNDpYMTSPAR   Arrestin beta 2 GMKDDDpYDDQLC  erbb2-interacting SATLLpYDQPLQVFTGSSSSS   protein DLISGTK  erbb2-interacting GPTSGPQSAPQIpYGPPQYNIQ   protein pYSSSAAVK  erbb2-interacting AQIPEGDpYLSpYR   protein   intersectin 2REEPEALpYAAVNK   isoform 1   LAIR-1 ETDTSALAAGSSQEVTpYAQLD HWALTQR   NCKadaptor LpYDLNMPAYVK   protein 1   p62dok1 Yes IAPCPSQDSLpYSDPLDSTSAQAGEGVQR   p62dok1 Yes EDPIpYDEPEGLAPVPPQGLpY DLPR   p62dok1 YesVKEEGpYELPYNPATDDpYAVP PPR   phosprot. assoc. ENDpYESISDLQQGR   GEM  “phospholipase C, Yes IGTAEPDpYGALpYEGR   gamma 1”   “phospholipase C,Yes NPGFpYVEANPMPTFK   gamma 1”   “phospholipase C, DINSLpYDVSR   gamma2”   “phospholipase C, RQEELNNQLFLpYDTHQNLR   gamma 2”   SHC YesELFDDPSpYVNVQNLDK   SHP2 interacting Yes SGESVEEVPLpYGNLHpYLQ   tmadaptor TGR   SHP2 interacting Yes SQASGPEPELpYASVCAQTR   tm adaptor  SHP2 interacting Yes ASFPDQApYANSQPAAS   tm adaptor   Wiskott-AldrichLIpYDFIEDQGGLEAVR   syn. protein‡ * indicates activation loop peptides.TCR indicates proteins with known roles is T cell receptor signaling.

About one-third (56 of 156) of the phosphotyrosine peptides found inthis sample originated from proteins with well-documented roles in Tcell receptor signaling. Among these were the tyrosine kinases ZAP70 andLck, which are activated by T cell receptor stimulation. Six tyrosinephosphorylation sites were found in ZAP70, including Tyr-493 in theactivation loop, and three sites were found in Lck, including theactivation loop site Tyr-394. All the tyrosine phosphorylation sitesfound in ZAP70 and Lck have been reported previously. Phosphorylationsites in the activation loops of two other tyrosine kinases and threeserine/threonine kinases were also found: the receptor tyrosine kinaseEphA4 and the cytoplasmic Fer tyrosine kinase, as well as activatedserine/threonine kinases p38 MAP kinase, GSK3 alpha, and PRP4. Inaddition, many phosphotyrosine-binding adaptor proteins involved insignal propagation were identified as tyrosine phosphorylated, includingp62dok1, NCK, SHC, SHP2, and the phospholipase C gamma 1 and gamma 2isoforms.

This demonstrates the method of the invention can be used to identifytyrosine kinases that are abnormally activated in cancer cells as wellas their substrates, including other protein kinases and adaptorproteins.

1. A method for isolating a modified peptide from a complex mixture ofpeptides, said method comprising the steps of: (a) obtaining aproteinaceous preparation from an organism, wherein said proteinaceouspreparation comprises modified peptides from two or more differentproteins; (b) contacting said proteinaceous preparation with at leastone immobilized modification-specific antibody; and (c) isolating atleast one modified peptide specifically bound by said immobilizedmodification-specific antibody in step (b).
 2. The method of claim 1,further comprising the step of (d) characterizing said modified peptideisolated in step (c) by mass spectrometry (MS), tandem mass spectrometry(MS-MS), and/or MS³ analysis.
 3. The method of claim 2, wherein saidmass spectrometry comprises MALDI-TOF MS, wherein said tandem massspectrometry comprises LC-MS/MS, and wherein said MS³ analysis comprisesLC-MS³.
 4. The method of claims 2 or 3, further comprising the step of(e) utilizing a search program to substantially match the spectraobtained for said modified peptide during the characterization of step(d) with the spectra for a known peptide sequence, thereby identifyingthe parent protein(s) of said modified peptide.
 5. The method of claim1, wherein said proteinaceous preparation comprises a digestedbiological sample selected from the group consisting of a digested crudecell extract, a digested tissue sample, a digested serum sample, adigested urine sample, a digested synovial fluid sample, and a digestedspinal fluid sample.
 6. The method of claim 5, wherein said digestedpreparation is obtained using at least one proteolytic enzyme orchemical cleavage.
 7. The method of claim 6, wherein said proteolyticenzyme is immobilized.
 8. The method of claim 6, wherein saidproteolytic enzyme is soluble, and wherein said digested preparation istreated with a proteolysis inhibitor prior to said contacting step (b).9. The method of claim 1, wherein step (a) further comprisespre-purifying said proteinaceous preparation by immobilized metalaffinity chromatography (IMAC).
 10. The method of claim 1, wherein saidimmobilized antibody of step (b) is covalently-linked to achromatography resin or noncovalently-linked to protein-A- orprotein-G-agarose.
 11. The method of claim 10, wherein said resin iscontained within a column or micropipette tip.
 12. The method of claim2, wherein said immobilized antibody of step (b) is immobilized inchromatography resin within a column, said column being coupled to amass spectrometer for said characterization of step (d).
 13. The methodof claim 1, wherein said modification comprises phosphorylation.
 14. Themethod of claim 1, wherein said modified peptide(s) comprise(s) aphosphopeptide.
 15. The method of claim 1, wherein saidmodification-specific antibody comprises a motif-specific,context-independent antibody that recognizes a motif comprising at leastone phosphorylated amino acid.
 16. The method of claim 15, wherein saidmotif consists of a single phosphorylated amino acid.
 17. The method ofclaim 15, wherein said motif comprises all or part of a kinase consensussubstrate motif or a protein-protein binding motif.
 18. The method ofclaim 17, wherein said kinase consensus substrate motif is selected fromthe group consisting of MAPK consensus substrate motifs, CDK consensussubstrate motifs, PKA consensus substrate motifs, AKT consensussubstrate motifs, PKC consensus substrate motifs,phosphothreonine-X-arginine, and ATM consensus substrate motifs, andwherein said protein-protein binding is a 14-3-3 binding motif or a PDK1docking motif.
 19. The method of claim 1, wherein saidmodification-specific antibody is a monoclonal antibody or a polyclonalantibody.
 20. The method of claim 1, wherein said modified peptideisolated in step (c) corresponds to a known marker of disease.
 21. Themethod of claim 4, wherein said modified peptide characterized in step(d) comprises an unknown modification site of said parent protein. 22.The method of claims 2 or 3, further comprising the step of (e)comparing the modification state of said modified peptide characterizedin step (d) with the modification state of a corresponding peptide in areference sample, thereby to compare protein activation in saidproteinaceous preparation with protein activation in said referencesample.
 23. The method of claim 22, wherein said proteinaceouspreparation corresponds to a diseased organism and said reference samplecorresponds to a normal organism, whereby comparison of proteinactivation provides information on activation changes resulting fromsaid disease.
 24. The method of claim 22, wherein said proteinaceouspreparation is obtained from a tissue biopsy cell or a clinical fluidsample and said reference sample corresponds to a diseased organism,whereby the comparison of protein activation provides information usefulfor diagnosis of said disease.
 25. The method of claim 22, wherein saidprotein preparation corresponds with an organism or preparation treatedwith at least one test compound and said reference sample correspondswith an untreated organism or preparation, whereby the comparison ofprotein activation provides information on activation changes resultingfrom treatment with said test compound.
 26. The method of claim 23,wherein the comparison of protein activation identifies the modifiedpeptide characterized in step (d) as corresponding to a parent proteinnot previously reported as so modified in said disease.
 27. The methodof claim 24 or 25, wherein said disease is cancer.
 28. The method ofclaim 25, wherein said test compound comprises a cancer therapeutic. 29.The method of claim 25, wherein said test compound comprises a kinaseinhibitor.
 30. A method for isolating a phosphopeptide from a complexmixture of peptides, said method comprising the steps of: (a) obtaininga proteinaceous preparation from an organism, wherein said proteinaceouspreparation comprises phosphopeptides from two or more differentproteins; (b) fractionating phosphopeptides in said proteinaceouspreparation by reversed-phased chromatography to produce a fractionatedproteinaceous preparation; (c) contacting said fractionatedproteinaceous preparation with at least one immobilized motif-specific,context-independent antibody that binds a motif comprising at least onephosphorylated amino acid; (d) isolating at least one phosphopeptidespecifically bound by said immobilized antibody in step (c); and (e)characterizing said phosphopeptide isolated in step (d) by massspectrometry (MS), tandem mass spectrometry (MS-MS), and/or MS³analysis.
 31. The method of claim 30, further comprising the step of (f)utilizing a search program to substantially match the mass spectraobtained for said phosphopeptide during the characterization of step (e)with the mass spectra for a peptide of one or more known protein(s),thereby identifying the parent protein(s) of said modified peptide. 32.The method of claim 32, wherein said mass spectrometry comprisesMALDI-TOF MS, wherein said tandem mass spectrometry comprises LC-MS/MS,and wherein said MS³ analysis comprises LC-MS³.
 33. The method of claim32, wherein step (a) further comprises digesting said proteinaceouspreparation to produce a complex mixture of peptides.
 34. The method ofclaim 30, wherein said motif-specific, context-independent antibody ofstep (c) comprises a general phosphotyrosine-specific antibody, ageneral phosphothreonine-specific antibody, or a generalphosphoserine-specific antibody.
 35. The method of claim 30, whereinsaid motif-specific, context-independent antibody of step (c) isspecific for a phosphorylated kinase consensus substrate motif orprotein-protein binding motif.
 36. The method of claim 35, wherein saidkinase consensus substrate motif is selected from the group consistingof MAPK consensus substrate motifs, CDK consensus substrate motifs, PKAconsensus substrate motifs, AKT consensus substrate motifs, PKCconsensus substrate motifs, phosphothreonine-X-arginine, ATM/ATRconsensus substrate motifs, p85 P13K binding motif,phosphothreonine-proline motif, Arg-X-Tyr/Phe-X-phosphoserine motif,phosphoserine/phosphothreonine-Phe motif, PLK consensus substratemotifs, and DNA damage-induced substrate motifs, and wherein saidprotein-protein binding is a 14-3-3 binding motif or a PDK1 dockingmotif.
 37. The method of claim 30, wherein said reversed-phasedchromatography of step (b) comprises a C18 column.
 38. The method ofclaim 30, further comprising the step of (f) quantifying said isolatedphosphopeptides of step (e).
 39. The method of claim 38, wherein step(f) comprises quantifying said isolated phosphopeptides using stableisotope labeling by amino acids in cell culture (SILAC) and/or absolutequantification of peptides (AQUA) techniques.
 40. An immunoaffinityisolation device for the isolation of modified peptides a complexmixture, said device comprising a support comprising at least onemodification-specific antibody immobilized to a rigid, non-porous ormacroporous resin.
 41. The device of claim 40, wherein said support isselected from the group consisting of a thin capillary column having aninternal diameter of about 50 to 300 micrometers and a micropipette tip.42. The device of claim 41, wherein said modification-specific antibodycomprises a motif-specific, context-independent antibody.
 43. The deviceof claim 41, wherein said column is adapted to be coupled to anelectrospray source on a mass spectrometer.
 44. An antibody that bindsubiquitin fusion degradation protein 1 (UFD1) only when phosphorylatedat serine 335, but does not substantially bind to UFD1 when notphosphorylated at this residue.
 45. An antibody that bindsprotein-tyrosine phosphatase 1c (PTN6) only when phosphorylated atserine 588, but does not substantially bind to PTN6 when notphosphorylated at this residue.
 46. An antibody that binds a proteinphosphorylation site listed in Column 5 of Table 5 only whenphosphorylated at the phosphorylatable residue indicated in Column 5,but does not substantially bind to the phosphorylation site when notphosphorylated at the indicated residue.
 47. An antibody that binds aprotein phosphorylation site listed in Column 5 of Table 6 only when notphosphorylated at the phosphorylatable residue indicated in Column 5,but does not substantially bind to the phosphorylation site whenphosphorylated at the indicated residue.
 48. An antibody that binds aprotein phosphorylation site listed in Column 4 of Table 7 only when notphosphorylated at the phosphorylatable residue indicated in Column 4,but does not substantially bind to the phosphorylation site whenphosphorylated at the indicated residue.